Full Service Payroll FAQ

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.

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).

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.

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

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

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

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.

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.

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.

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.

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 

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.

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.

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.

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!)

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.

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

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.

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.

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.

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.

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

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.

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.

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.

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.

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.

Absolutely.