It depends on whether you have turned on syncing payments in ContractorTools.
If "Sync Payments" is turned on in ContractorTools, then you should not enter a payment in ContractorTools if you receive the payment by credit card in QuickBooks.
If "Sync Payments" is turned off in ContractorTools, then you will need to enter a payment in ContractorTools if you receive the payment by credit card in QuickBooks.