I appreciate the complete details you've shared, @Gauchofife.
The late fee depends on the type of your payroll subscription and method. You can create a paper check so you'll not be charged for a late payments. Let me share some information on how this works.
First, it's possible that you're subscribed to Assisted payroll subscription. You can refer to this article for more insights: Assisted payroll ancillary fee schedule.
As a work-around, you can run a paper check so that you can run a paper check for it and give to your employee. First, you'd want to set the Termination status of your employee.
Once completed, you can now generate a paper check as the employee's last payroll. Here's how:
- Go to the Employees menu.
- Select Pay Employees.
- Choose Unscheduled Payroll.
- Enter the payroll info, and then click Continue.
- Review your employee's payroll details.
- Make sure to remove the check-mark on the Use Direct Deposit tick box.
- Click the Create Paychecks button.
Now, you can run payroll-related reports to ensure the accuracy of your records. To do this, go to the Reports menu, and then select the desired report from the Employees & Payroll section.
You're always welcome to get back here in the Community if you have more questions about managing your payroll in QuickBooks Desktop. I'll be here to help.