You'll go into Receive Money just like you would for a check from a customer, but to the left of where you enter a customer ID you can change it to Vendor ID. Then enter the ID of the vendor you got the refund from. Complete the rest of the top half of the screen like you normally would. On the "Apply to Vendor Accounts" tab you can enter a description if you want to but don't change the GL Account. Enter the amount if you didn't enter it at Receipt Amount. Save the transaction. This will now show up on the vendor's account like an invoice.

If you have already entered a credit memo from the vendor for the over-payment, then go to Payments (AKA Pay Bills) and enter a dummy payment to this vendor. Select both the credit memo and refund, the amount should total to zero.

If you don't have a credit memo you'll need to enter one using the Vendor Credit Memo screen. The amount should go on the "Apply to Purchases" tab. The GL account should be the expense account from the over-payment, or if there were inventory items involved with the over-payment, use the same items and quantities here.