Agricultural Employers need to use a 943 form rather than a 941, but Quickbooks Payroll doesn’t support making 943 electronic deposits. So here’s the workaround:
1) Sign on directly to the EFTPS site:
https://www.eftps.gov/eftps/direct/EftpsHome.page
and make the payment there, indicating it is for form 943.
2) Then, in Quickbooks, record the payment. Choose Employees > Payroll Taxes and Liabilities > Create Custom Liability Payments, In the Select Date Range for Liabilities window, enter the date range for the tax liability payment and click OK
3) n the Pay Liabilities window, select the tax liabilities you want to pay and click Create, to enter a “check” in QuickBooks, using the EFTPS receipt number as the Check #, so that the debit to your bank account is recorded. Make sure that you uncheck the “To be printed” box on the check form. The offset will be the payroll liabilities that you selected in step two.
You may want to make the payment on the EFTPS site after “creating” the check, so that you have the exact amount, but go back and add the receipt # to the check so that you have a good trail of your payments.
Finally, use the Send Feedback Online link under the Help menu to request that Intuit add this ability to its payroll offerings!