You to make the books exactly match what happened. No other choice. ;-) So, you need to delete the payment that the other person entered and showed as deposited in December. That will throw your bank balance off, but you'll fix it next. Change the November payment that you entered to the exact amount that went through the credit card in November - and show that as deposited to the bank account (assuming your credit card processor did credit the bank in November). Verify that the November bank statement now reconciles, and that the Customer shows an amount outstanding equal to what they paid in December for the balance. If that's all good, go ahead and enter a Receive Payment for the credit card, going to your bank account, in December for the actual balance received in December. The Customer and Bank accounts should not reconcile.
If your credit card processor aggregates credit card changes and credits the bank with some total of multiple transactions, then in future you'll want to put those charges in Undeposited Funds, and 'deposit' them when the credit card processor transfers the balance, less fees, to your account.
If your processor is Intuit, then there is a separate interface for depositing your credit card payments which automatically credits the customer with the full payment, and then allocates the merchant services fees to the appropriate expense account and the balance of the payment to your checking account. Moving forward, you'll use that interface ... if Intuit is your merchant services provider. But, to fix this, you'll need to adjust/enter the fees/etc yourself clear the customer balance, and deposit the correct amount to your checking account.
As best as I can tell from what you've said. ;-)
