I've got some steps on how you can record the 940 tax payments in QuickBooks, lilavalv.
It's great to know you paid the tax payments on time through the EFTPS website. To record them in the software, we need to open the 940 liability and apply for the payment on it.
Click Employees on the top menu.
Choose Payroll Center.
Hit Pay Liabilities.
Select Federal 940.
In the Memo column, enter that the payment already made in the EFTPS.
Tap Save & Close.
If you already created a check in QuickBooks, you can record the tax payments by not affecting the bank account. This way the prior payment will not show up in the bank register since your checking account has the correct balance.
Click Help on the menu and choose About QuickBooks.
Press Ctrl + Alt + Y or Ctrl + Shift + Y to open the Setup YTD Amounts window.
Hit Next until you reach the Enter prior payments section.
In the Enter Prior Payments window, tap Create Payment.
Enter the Payment Date and For Period Ending date accordingly (in many cases these dates will be the same).
In the Taxes and Liabilities field, choose the Federal Unemployment tax item that you've already paid and want to record in QuickBooks Desktop. And enter the amount. You can add a memo to remind you what the payment is for
Tick the Account Affected button and select test the Affect liability accounts but not the bank account option. Then, OK.