Hi AMR,

Since the original post, Intuit has added a feature to make the credit card management easier and less confusing.

To pay the credit card, go the that register and do New, Pay Down Credit Card. This way you an confirm what account you want to pay it from. (This is, in effect, a transfer from one bank account to another.)

To get the expenses in there, set it up to get the bank feed for the credit card. When the transactions come in, make sure in Review you are getting the categories correct (set up Rules wherever it makes sense).  

Then when you go to reconcile the cc each month, all will be good.

Hope this helps and that I'm understanding your question correctly.