To record the refund check, go to Tasks > Receive Money. Change "Customer ID" to "Vendor ID", then enter the vendor ID where you would normally enter your customer. Everything else in the header gets filled out like normal. Enter a description if you want to but don't change the GL account.

After you save the receipt, go to Tasks > Payments. Enter a dummy check and select both the refund you just entered and the credit that was being refunded. The check amount should be zero.