You need to treat your credit card like a separate (overdrawn) bank account on QuickFile. Don’t try to split up all the items on your primary business account as you will run into the exact problem you described in regards to date discrepancies.
So essentially you have the separate Credit Card bank account on QuickFile with all payment activity specific to that card, tag it up against all your purchases. Then when you pay down your card balance at the month end, treat this as a bank transfer from your current bank account to the Credit Card account.
It’s the same way in which you handle payment providers like PayPal. We have a guide on managing credit cards in QuickFile here:
http://community.quickfile.co.uk/t/managing-credit-cards-in-quickfile/8845