Did you do this through the Download Transactions window for your Bank Account (online banking)?  If so, when you added the payment to the register you'll want to make sure the offsetting account is your Credit Card Account.  This will create the check between the two accounts showing it as a payment against the Credit Card Account.  I've attached a sample picture of what it should look like in the Bank Account register after downloading/recording the payment.  Then you will not have to add the payment in the Credit Card register, ti should already be there for you.