How do I handle "uncleared payment" recorded as a Transfer and another recorded as Credit Card Payment. Journal Entry Debiting Quickbooks and crediting the credit cards?

Was this through Bill Pay or just an entry in the Checking Account Register?  And why is it not clearing when you do your regular monthly Reconciliation of the Checking Acct and the Credit Card Acct? 

If it's a Bill Pay issue, it should like you did not actually pay the bill through the system.  So you just need to go to New > Pay Bill and make the payment (be sure to use the date you actually paid on).  This will probably create duplicate entries, so go back into the Checking Register and delete the original incorrect payment.  This should also then remove the incorrect payment from the CC Register.  You should then have a Paid Bill and the correct transactions in the two Registers. 

If this is not what happened, give us some more info.  JE are the last thing to go to in my opinion for these kind of things.  Much better to get them entered in correctly so there are no questions sometime in the future.