Full Service Payroll FAQ

What is Full Service Payroll?

We will deposit and file all your applicable federal, state, and local payroll taxes.

Why do I need Full Service Payroll?

Payroll tax management can be challenging for small business owners who are juggling their daily operations, and just one missed payroll tax deposit can result in fines and penalties. Our small business payroll tax service wipes away your worries about payroll tax management and allows you to focus on the business at hand.

How do I know everything will be done correctly?

We guarantee the accuracy and timeliness of our work, based on the tax rates and deposit frequencies you select. A history of the tax deposits and filings that we’ve done on your behalf is provided to you online so you can see for yourself!

How do I start using Full Service Payroll?

To get started today with our corporate payroll solutions, complete our short sign-up form. For a video demo, a quick rundown on the info you’ll need to set up payroll (or we can set it up for you) and more, visit the Getting Started page.

How does the 30 day free trial work exactly?

We may make one or more Services available to you on a limited time trial basis free of charge.

Your 30-day free trial begins once you click “Start Free Trial”. We won’t actually withdraw (ACH) fees until the end of your trial. If you cancel your subscription in your first month you will not be charged. If you don’t cancel by day 30, your account will be debited for the amount from the fee structure for the software and/or services you use each month. You can cancel your full-service payroll subscription at any time.

Any data you enter into the Software during a free trial may be permanently lost unless you provide a valid credit card for payment or export your data before the end of the free trial. All free trial Services are provided “as is” without any warranty.



What happens if I add Full Service Payroll mid-year?

If you start using our payroll tax filing service in mid-year, we’ll collect from you all tax liabilities you haven’t yet deposited and hold them in escrow until it’s time to deposit them. From then on, we’ll start collecting the tax liabilities as you run payrolls. Adding Full Service Payroll at the beginning of a quarter or a year will make for a much easier transition for your business.

How do I pay for Full Service Payroll?

To pay for the TransNational Payments tax filing service, you will need a valid credit card. Payroll taxes will be drawn from a validated bank account which you provide.

What if I run payroll for employees in more than one state?

Our pricing reflects tax filing in one state. There is an additional fee of $12/mo for each additional state.

What is the cloud?

The cloud, as in cloud computing, is simply an industry term meaning computer programs or applications that you can access on the internet. With our corporate payroll solutions, your payroll data is securely stored on our secure web servers instead of your personal computer. You don’t need to worry about backing up your payroll data on your own hard drive. If your computer fails, your payroll data is still safe with us.

Cloud computing technology also makes it convenient to run payroll anywhere you are. For example, if you forget to run your weekly payroll at the office, you can still pay your employees from the comfort of your living room with our payroll software.

How does Time & Attendance Software/Human Resources Software work?

Please visit the Time & Attendance page or the Human Resources page for features and related FAQs.

Do you offer a way for me to provide my employees with paper checks?

Yes. You can set it up through the software that you are either handwriting or printing your own paychecks. If you want to hand write the checks and print a stub through the software you can. You can also print your own checks through the software using check stock paper.

Do you supply the check stock paper? Is there an extra charge if I print checks?

We do not supply check stock paper. We do have a vendor called Carousel checks that we recommend getting check stock from:
There is no additional charge if you would like to print your own checks

What if I receive a notice stating my deposits and filings weren’t properly handled?

There may be several reasons for this notice. The first is that you haven’t set up the proper deposit frequency. In this case, you should immediately change the deposit frequency in the software, and then contact the tax agency to resolve the issue. The second possibility is that we might have made a mistake. In that case, please call our Customer Support at (877) 968-7147. We’ll handle the corrections and take responsibility for all applicable penalties and interest.

What types of deposits and forms do you handle?

Our Full Payroll Service is perfect for small businesses and handles all employee taxes and most of the employer taxes, including federal, state and local taxes. We do not handle household employers (Schedule H).

Do you handle Workers' Compensation Insurance?

TransNational Payments collects and files Workers’ Compensation Insurance for Washington and Wyoming. To provide Workers’ Compensation insurance coverage to other states*, TransNational Payments has partnered with AP Intego. AP Intego offers affordable Pay As You Go (PAYG) Workers’ Compensation Insurance. Please contact us for more information on pricing.

*Important: North Dakota and Ohio are required to obtain Workers’ Compensation insurance through their own state funds, therefore TransNational Payments cannot offer Workers’ Compensation insurance as an add-on to Full Service Payroll in these states.

Do you handle the transferring of funds for insurance, garnishments, retirement contributions or child support?

No. While you can set up custom deductions and contributions, TransNational Payments DOES NOT handle the remitting of these funds to the proper agencies.

Do you handle the IRS form 943 Employer’s Annual Federal Tax Return for Agricultural Employees?

No. TransNational Payments DOES NOT handle the IRS form 943 for Agricultural Employees.

Does the payroll software handle expenses and supplemental pays?

Yes. You have the ability to set up pay codes for handling expenses, supplemental pays and other “dollar-related” types of money.

How does the payroll software handle deductions?

You can set up an unlimited number of payroll deductions to be used by your company, both taxable and non-taxable. When setting up deductions, you can define specific dollar amounts or percentages. When you add a deduction to an employee, your deduction setup will automatically be applied on each payroll run. You may also define deduction stop limits in the payroll system to ensure a payroll deduction automatically stops once a certain amount has been deducted.

Can you calculate our company’s contributions towards employee benefits, such as 401k or health insurance?

Yes. With this payroll system, you can set up an unlimited number of company contribution rules. These rules will calculate your company’s match toward benefits (i.e., 401k matching, employer share of medical insurance, etc). When setting up contributions, you can define specific dollar amounts or percentages. When you add a contribution to an employee, your setup will automatically be applied on each payroll run.

How long does it take to pay employees with the software?

It depends on the number of employees you have and how many different types of hours and money you are using. With our payroll system, you can pay your employees in just a few clicks.

Can you handle tracking vacation and sick time off?

Yes. You can keep track of “buckets” of non-worked hours for each employee, such as vacation or sick time. You would add hours to their bucket, mark the date and number of hours the time was taken, and the available balance will be tracked for you.

Can you automatically set up time off accrual rules?

Yes. You can assign these rules to employees to automatically calculate time off hours given each time you run a payroll. For example, you can set up a rule to earn 1 vacation hour for every 40 hours worked.

You can find the company-level time off accrual rules in the “Payroll Settings” on the “Settings” page:

Settings > Payroll Settings > Time Off Accruals 

I can't remember my Merchant Portal password. How do I reset it?

No need to call Customer Service! Simply go to the Merchant Portal log-in page , click “Forgot your password?” and check your email inbox for an email from Patriot Software with a link to reset your password.

What does Full Service Payroll include?

If you are a Full Service Payroll customer, we will handle all the necessary collections for your payroll tax deposits, and filing (reporting) of ALL applicable Federal, State, and Local taxes that you have set up in the system. This includes creating and submitting the 940 and 941 Filing payroll tax filing forms needed at quarter-end and year-end. Unlike other payroll software providers, we won’t send you forms that you have to sign, seal and deliver. We will submit all of your forms to the appropriate taxing agency for you, so when you see them, they’ll be finished! And, we include ALL state and local taxes that might be applicable.

Who will be responsible for filing our payroll taxes?

If you are a Full Service Payroll customer, and have completed the set-up tasks for the payroll tax filing service, we will handle the calculation, collection, remittance and filing of your payroll taxes.

What is deposit frequency?

Deposit frequency is how soon you need to deposit your tax liabilities following a payroll run. The tax agency determines your deposit frequency. For example, depending on your payroll size, the IRS may decide your business should file monthly deposits and require your federal payroll tax liability (941) for November to be deposited by December 15. As far as the IRS is concerned, you’d be considered a monthly depositor, but other tax agencies may require different frequencies. (That’s why it’s just easier to let us keep track of it all through the payroll tax filing service!)

Where do I find my account numbers for payroll tax filing?

You can find account numbers on the pre-printed forms, tax coupons or any correspondence from the taxing agencies. Contact them if you don’t have the official forms or coupons.

What do I do if I don’t know my account numbers?

If you don’t know your account numbers, you can temporarily mark your account number as “applied for” in the software, but you’ll need this information before any payroll tax filings or deposits can be properly handled. When we are handling your payroll tax filing or depositing tax liabilities, we need the account number to eliminate confusion with the tax agency. If we don’t have the account number in time, we’ll still make timely deposits and payroll tax filings on your behalf, but you’ll need to add your account information. To make your life easier, try to gather this info when you first sign up with our Full Service Payroll.

What do I do with rate change notices?

Sometimes you may receive a rate change notice on taxes. If this happens, and it is a tax that you manually entered into the software yourself, you must enter the rate change yourself. This only applies to employer taxes such as varying unemployment rates (such as SUTA), which are based on each employer’s experience rating. Note: When changing a rate in the payroll software, indicate the proper start date for the changed rate. For specific instructions, see the training article Updating your State Unemployment (SUTA) Rate.

On the other hand, our software automatically adjusts when a global tax rate changes or a new tax goes into effect. With the Full Service Payroll, we automatically update global rates that don’t vary for individual employers, such as federal, state and local income tax rates.

What happens if I don’t know my deposit frequencies?

Our software knows the different deposit frequency options for various tax agencies and will narrow down your options. If you don’t know your deposit frequency, choose the frequency that happens most often. When you have the exact info, please enter the proper frequency so we can get your deposits on track.

What does “allow courtesy” mean?

Your employees may be liable for payroll tax filing where they live. It’s not always your responsibility to deduct these taxes from their pay and make deposits on their behalf, but you can as a courtesy. If you “allow courtesy,” you (the employer) must register for account numbers in all additional tax jurisdictions so the payroll tax filing service can file and deposit these taxes for you. For more information, see our software training article Courtesy Tax Withholding on the Patriot Software site.

What will happen if I select “allow courtesy”?

Our software will determine if your employees are responsible to pay taxes based on where they live. TransNational Payments withholds these taxes from the employee and deposits and files the taxes. As the employer, you’ll need to register for account numbers in all additional tax jurisdictions so TransNational Payments can comply with the payroll tax filing and deposit regulations.

Who’s responsible if I’m assessed for any penalties and interest?

With TransNational Payments as your payroll tax filing solution, you can rest assured that we will cover all interest and penalties if we are at fault for an error. If the error was yours, then you simply call the taxing agency and correct the errors. Make sure you remember to make any corrections in the payroll software to avoid repeating the error. Feel free to call us at (877) 968-7147.

When are my tax returns filed and how does TransNational Payments know when to file them?

We use the deposit frequency and general filing rules that tax agencies have set up to properly file your returns. Each tax agency has its own rules about when tax returns should be filed. TransNational Payments knows the timing and format in which your specific tax agencies require filings.

When are payroll taxes withdrawn?

After you have completed your tax filing setup, TransNational Payments will collect payroll taxes on approved payrolls usually the first banking day before the pay date. If payroll is run on the same day as the pay date, payroll taxes will be collected on the next available banking day.

When are my tax liabilities deposited?

Each tax agency may have its own deposit frequency. Based on the tax jurisdiction and deposit frequency you select, TransNational Payments will file (“report”) your payroll tax liabilities at the correct time. During setup, you’ll indicate the frequency of tax deposits for each tax.

How can I find out if my payroll tax filings and deposits were properly filed and deposited?

You can see which taxes we have deposited and filed on your behalf using various reports in the software. However, it’s good sense to follow up with the tax agencies to confirm the payroll tax deposits and filings are being made. Ultimately, it’s your responsibility to verify your taxes are being filed and deposited properly.

What W-2 or W-3 forms are there?

The W-3 form is submitted to the Social Security Administration. (We will submit this for you, but we suggest printing a copy of the W-3 for your records.)

There are multiple versions of the W-2 forms, each intended for a different recipient:

  • The W-2 Copy A is submitted to the Social Security Administration. (We will submit this for you!)
  • The W-2 Copy D or W-2 Copy 1 is for you (the employer) to keep OR submit with the EMPLOYER’S state, city or local tax return.

Be sure to give your employees the following:

  • The W-2 Copy B is to be submitted by the EMPLOYEE for their federal tax return.
  • The W-2 Copy C is to be kept by the EMPLOYEE for their records.
  • The W-2 Copy 2 is to be submitted by the EMPLOYEE to their state, city or local tax agency.

How are quarter- and year-end forms (940, 941, W-2, W-3) handled?

TransNational Payments will submit your 940, 941, W-2 and W-3 data to the proper tax agencies each quarter-end and at year-end. Just print out the W-2 forms to hand out to your employees. We’ll give you detailed info on where to buy blank W-2 forms so that you can print them out using your printer.

Please note: if you’re NOT a Full Payroll Service client, we’ll still give you access to the form data, but we won’t submit any information on your behalf.

When does TransNational Payments debit money from my account for my payroll tax liabilities?

Once you process your payroll, you immediately receive an invoice; the invoice date tells when the tax liability funds will come out of your account. You should have the funds in your account at least one business day before the date on the invoice. (Note: If you ever run a same-day payroll, you must ensure funds are available that day for your liabilities.)

A word about insufficient funds …
We hope this will never happen … but in the case of insufficient funds, we’ll contact you right away to make you aware of the problem. We may limit your use of the software until the issue is resolved. Please refer to your service agreement for information on applicable charges.

We will not be responsible for banking charges or penalties you incur as a result of insufficient funds, nor are we responsible if we must pay your tax payments late due to insufficient funds.

Do tax liability deposits that come out of my account go straight to the tax agencies?

No. When you accept a payroll, we’ll collect the tax liabilities then and hold them in escrow so they’ll be available when we need to deposit taxes on your behalf. In this way, you can better manage your cash flow, and we can ensure your liabilities are properly paid and on time.

Do you offer direct deposit?

Yes! We offer free direct deposit of paychecks to employees.

How does direct deposit work?

We allow you to set up unlimited direct deposit accounts for your employees. When you run a payroll, we will generate pay stubs (instead of live checks) for those employees with direct deposit showing their payroll detail. We will then deposit the employee’s pay directly into their bank accounts on pay day.

What are the advantages of using direct deposit?

Convenience: You can offer free direct deposit of paychecks to any or all of your employees. Money is deposited in employee bank accounts on pay day without any trips to the bank or ATM. You as the employer no longer have to print or reconcile paper checks.

Automatic: We will withdraw funds from your bank account and distribute the money to employee bank accounts on your chosen pay day. There is nothing else you need to do each payroll.

What is the lead time for direct deposits?

We offer two options for direct deposit:
Option 1: Four days before payday with regular ACH funding. Your money will be ACH debited from your bank after you run payroll for the actual amount of your payroll.

Option 2: Two days before payday with pre-funding. You will designate a scheduled dollar amount to be debited before you run payroll. We will compare the amount debited with the actual payroll amount. If the payroll exceeds the pre-funded amount, we will automatically debit the difference, depending on the overage. Any amount over the actual payroll is credited back to your company’s bank account two business days after payday.

How do I sign up for direct deposit?

As a Payroll customer, you can sign up while logged into your account. You will complete an application and upload your commercial/business bank account statement.

Can I use a personal bank account for my direct deposit?

We will only accept applications from small business owners using a commercial/business bank account for their payroll.

What does it cost to use direct deposit?

There is no charge for using standard direct deposit services with us. However, there are charges for non-sufficient funds, or if corrections are needed. Any fees you incur for direct deposit corrections will be charged to your credit card.

How do I fund the direct deposits?

The most common method is to directly withdraw the net payroll amounts from your bank account and make the deposits into the employee bank accounts.

Can I cancel Full Service Payroll at any time?

You can cancel payroll tax filing anytime, but the timing may affect the ease of your transition to another tax service provider. Cancelling at the end of a quarter would be ideal. Your new provider may charge additional fees if the transition happens mid-quarter or mid-year. Call our Payroll Partner Success Team at Patriot Software (877) 968-7147 for help and advice with this transition. In addition, cancelling your payroll may impact your fees on our payment processing service.

What happens if I cancel Full Service Payroll mid-year?

If you cancel our payroll service, we’ll stop collecting tax liabilities on the chosen date, and return any tax money collected that hasn’t been deposited. TransNational Payments will submit filings related to any payrolls that occurred before your cancellation (even if the filing due date falls after your cancellation date). But we won’t be responsible for payroll tax filings related to any payrolls that happen after your cancellation date.

How do I cancel my free trial?

To cancel your free trail please call our Payroll Partner Success Team at Patriot Software, 877-968-7147.

We may make one or more services available to you on a limited time trial basis free of charge.

Your 30-day free trial begins once you click “Start Free Trial”. We won’t actually withdraw (ACH) fees until the end of your trial. If you cancel your subscription in your first month you will not be charged. If you don’t cancel by day 30, your account will be debited for the amount from the fee structure for the software and/or services you use each month. You can cancel your full-service payroll subscription at any time.

Any data you enter into the Software during a free trial may be permanently lost unless you provide a valid credit card for payment or export your data before the end of the free trial. All free trial Services are provided “as is” without any warranty.


If I cancel my payroll services, do I have the option to stay with TransNational Payments for my payment processing?


Ready to save time and money on your next payroll?