I'd be pleased to help you with entering credit card overpayment refund in QuickBooks Desktop, ChiColorLabel.
You can use the Enter Credit Credit Charges option to record and reflect the credit properly on QuickBooks Desktop. Here's how:
For your reference, check out this article: Record a vendor refund in QuickBooks Desktop. On the same link, you'll find scenarios about how to handle vendor refunds as well as steps to record them.
Should you need additional assistance, please let me know. I'd be more than willing to lend you a hand.