Hi jhubbard,
You'll want to resolve the overpayment first. After that, you'll want to open the 940 form again.
- Go to Taxes.
- Choose Payroll Tax.
- Review the list of 940 payments on the Pay Taxes page. An overpayment has a negative amount.
- Click on Resolve Overpayment.
- You can choose to get a refund.
- Click on Mark as resolved.
- Contact the IRS to get a refund or apply the overpayment to the next tax period.
You can check the article about resolving overpayments for additional reference.
Please let me know if you need more help.