This is a common situation of confusion... no matter which version of QuickBooks you're using, because it is a bookkeeping question really. ;-)
It sounds as though both your checking account and your credit card account have been set up in QuickBooks. Assuming that is the case, this is how it should work:
You would "categorize" each of the transactions (charges) on the credit card account (as they came in) to their appropriate expenses (so you capture the tax deductions).
You would next "categorize" the payment you made to the credit card from the checking account to the account you've set up for that credit card (not an expense account). In essence, you are just transferring the money from the checking account to the credit card account to pay for the purchases already recorded.
Whether you download the transactions or enter them in manually, the principles are the same. While this is showing how to do it in QuickBooks desktop, if you grasp the principles of how it works, you can use it to properly code your downloaded transactions in QuickBooks Online.
http://qbquicktips.com/blog/general/credit-card-accounts-in-quickbooks/ Hope this helps. :-)
