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.

Please see this article for a full explanation of syncing payments in QuickBooks.

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