How do I enter an overpayment to a vendor?

Hello there, @Aprilf100.

When you pay the same vendor's invoice twice, you need to record two (2) payments (through check and credit card) in QuickBooks Desktop (QBDT). Since you already entered the check, you can create a Credit Card Charge transaction to record the credit card payment. Here's how:

1. Go to the Vendors menu.
2. Select Vendor Center.
3. Choose the vendor's name to view their information.
4. Go to the Transactions tab.
5. Select Credit Card Activities in the Manage Transactions drop-down button.
6. Enter all the necessary details needed.
7. Click Save & Close.

I've attached screenshots below that show the last five steps.

Then, once you receive a refund, you'll have to deposit it to the vendor's A/P account. This way, you're able to apply the deposit and the bill payment to the check.

Also, you can run the Vendor Balance report to know what payments that make up each bill in QuickBooks. Just go to the Reports menu, select Vendors & Payables, then choose Vendor Balance Detail.

Please let me know if you have other concerns about managing vendor bills and payments in QBDT. I'm just around to help. Take care always.