This is quite a common accounting scenario. Essentially you treat your card service provider (e.g. Streamline, BarclayCard, Paypal, Stripe etc) as a bank in QuickFile.
You can log a bulk card sale invoice (e.g. weekly, daily or monthly) to the merchant bank account, then make transfers from here to your current account when you receive the funds. There would usually be a difference that would equal your payment provider’s charges, these can be logged as supplier invoices and paid from the merchant account.
We have more general guidance on this topic here: