QuickBooks Desktop doesn't support 943 payments. That is why the IRS posted the EFTPS payments under 941.
Since the EFTPS payment is already posted in the 941, we're unable to correct it in QuickBooks. We can send your payments directly to the IRS through the EFTPS website.
If you'd like to track your liability payments for the 943 taxes in QuickBooks, you can record it by setting up a payment schedule for the 941 taxes. To know more about setting up a scheduled liability in QuickBooks Desktop, see this article: Set Up and Pay Scheduled or Custom (Unscheduled) Liabilities
Alternatively, you can create your custom liability payment by following the steps below:
Go to the Employees tab.
Select Payroll Taxes and Liabilities.
Choose Create Custom Liability Payments.
In the Select Date Range for Liabilities window, enter the date range for the tax liability payment.
In the PayLiabilities window, select the tax liabilities you want to pay then click Create.
Also, you can use the Excel worksheet that contains data required in Form 943 to file with the IRS.
Here's how you can get the information:
Click the Reports menu, then go to Employees & Payroll.
Go to More Payroll Reports in Excel, then choose Tax Form Worksheets.
Enable/Turn on Macros.
The QuickBooks Tax Worksheets window will pop-up, choose Annual 943.
Enter the dates in the From and To fields, then click Create Report.
Once you're done, you'll have yo download the form from the IRS website. Manually enter the information, then re-submit it.