Think of your credit card account as a checking account, only in reverse.  Instead of you having money in the bank, you owe money to the bank.  But you want to go through the same process as a checking account.  Enter all your credit card charges as you go along and then reconcile your account once you get your statement.

I can’t know for sure without looking at your file, but I’m guessing you didn’t use your credit card account as the Account on the EFT check.  It’s also possible you didn’t use your credit card account when you paid the bill.  Credit card should be selected as Method and the correct credit card account should be selected in Account.