Quarterly, you must complete and submit a federal payroll tax return using Federal Form 941, which identifies the total wages you paid, when you paid them, and the total taxes you withheld and deposited with appropriate taxing authorities throughout the quarter. The IRS permits you to file the form electronically or to mail the form.
In this case, I'd suggest filing your forms manually to avoid further delays. Once done, you can archive the forms on your QuickBooks so it will be recorded as filed.
To do that:
In the navigation bar, click Taxes.
Select on Payroll Tax.
Under Forms, click the appropriate form category.
Click the form you want to archive.
Choose the liability period.
Make sure the correct form is displayed in the Adobe Reader window, and then close the window.
To give you complete details about this process, please refer to the following links below: