Hi there gremoo,
It's vital that all your transactions are entered correctly for your books to be well balanced. QuickBooks Desktop is a great tool able to help you keep track f the amounts you've paid in expenses and received as sales so you can see the profitability of your business. I can point you in the right direction to enter a credit on your credit card.
in order to enter a credit back to your credit card, you'd need to follow the steps in the fifth scenario of this article about entering supplier refunds. If you're still needing assistance with entering the credits so they appear correctly, I recommend reaching out to the QuickBooks Desktop support team outside of the Community. They'll be able to view your transactions with you in a secure setting in order to help you in getting those credits to appear correctly in your books. You can reach them using the steps in the QuickBooks Desktop software support policies.
If you have any other questions, feel free to reach out here.