I'm glad you've reached out to us. Let me help walk you through on how to record an overpayment for your employee.
When payroll liabilities are overpaid, the liability balance becomes negative. Since you've got a refund, you can record a refund check to increase the balance that'll correct your Payroll Liabilities.
First, you'll need to run the Payroll Liability Balances report to check for credits (amounts with negative values) that match the amount of refund and the tax item.
Once you created the employee's paycheck, under Other Payroll Items, select the addition item you created, then enter the amount. That should adjust the amount on the paycheck of the employee.
If you need further assistance with the steps from our live support, I encourage you to contact our QuickBooks Desktop Payroll Support Team. They have the tools to pull up your account and do remote session.