For a federal 941 payment that is normally done through E-pay, a physical check was written. How to mark it as paid and remove it from current tax liabilities?

Hello, @drbickley1.

You'll want to go to the Payroll Center tab and mark the liabilities from there. Here's how:

1. Go to the Employees menu, then select the Payroll Center.
2. Select the Pay Liabilities tab.
3. In the Pay Taxes & Other Liabilities section, mark the liabilities you want to pay, then press View/Pay.
4. Make sure the date and amounts are correct.
5. Click Save and Close.
6. Hit Print if you want to print the check.

Once you already mark the liabilities as paid it will remove directly in the Pay Taxes and Other Liabilities column. All the payments that you've made will show under the Payments History column and the check will mark as Cleared.

Also, you can can set up and pay scheduled or custom (unscheduled) liabilities. This way, you can set reminder notices and pay the liabilities as it's due. 

If you'll want to run payroll in the future, you can see this link. It includes information about payroll items assigned to a liability account, most deductions, and most company contributions. 

Please let me know if you have any other issues or concerns. I'm more than willing to help. Stay safe.

How do I pay late penalty fee for 941 from an IRS notice?

There are two options on how you can pay your penalty fee, @mlanclos.

You can pay it by creating a company liability adjustment in QuickBooks Desktop (QBDT). Let me show you how:

1. Go to the Employees menu and select Payroll Taxes and Liabilities.
2. Click Adjust Payroll Liabilities.
3. Enter the Date and Effective Date and select the Company button for adjustment.
4. Select the payroll item in the ITEM NAME drop-down list, then fill in the rest of the information.
5. Click OK.

After creating the liability adjustment, the amount will automatically show up in the Pay Liabilities section. Then, you can now proceed to creating the liability check to pay your penalty fee. Just select the 941 taxes and click ViewPay. Once done, you can print it and send to the IRS.

Your other option is by paying it directly to the IRS website. All you need to do is to go to this link: https://www.eftps.gov/eftps/.

Also, you can run the Payroll Liability Balances report in QuickBooks. This will show you the information about payroll items assigned to a liability account, most deductions, and company contributions.

If you have further questions or concerns, feel free to reach back out anytime.