Getting paid by credit card has many benefits: you have money in your account sooner, and you spend less time chasing invoices.
When you receive credit card payments into your bank account, it will show as a deposit from Fergus Payou, and the deposit will likely be for multiple invoices.
(It may show as Fergus Payou depending on your bank).
The quickest way to reconcile this deposit against your invoices is to consult the Fergus Pay Report found in the Reports menu.
Click Show to the right of any deposit and you will see a breakdown of which invoices this deposit covers.
Use this information to reconcile against your invoices like usual in your connected accounting package.