UPDATED: ***FOUND POTENTIAL ANSWER***
I will leave my original question at the bottom, it wouldn't let me reply to my own question. Everything I researched in the QuickBooks community said you couldn't do anything with 943 and e-payments using QuickBooks.
Attached is a screenshot of what we believe the solution is after researching another of our clients QuickBooks that we knew used e-pay to make Federal 943 Tax Deposits, but didn't know how our former ProAdvisor set them up. Please note this client has been doing it this way for years and has never had any notices, in case someone believes this could be a mistake as well.
My client uses QuickBooks Desktop. They are a 943 employer and pay their payroll taxes through QuickBooks.
QuickBooks is remitting the payment as a 941 rather than 943. They have received a notice showing they owe for payroll taxes because of this. How can I make the payments in QuickBooks show as 943 rather than 941?
You're correct, hannah-howard.
The option to e-file/e-pay Form 943 is unavailable in QuickBooks. However, you can use the Excel worksheet that contains data required in Form 943 to file with the IRS.
Then, download the form from the IRS website.
Meanwhile, you can continue using the Federal 943 Tax Deposit as the reason when recording your liability payment for tracking purposes.
Let me know if you have additional questions, we're always here to help.