What is the preferred method for registering a Customer Invoice (Instant or Customer Order) and then registering it has been paid by credit card?

Hi, 

Typically, the process would be to create a cash account (not GL account) and use this when performing a payment transaction. For example, set up a cash account as CC Pay. Then in posting control set PP1 (Cash) where CC Pay will hit GL account XYZ (the correct account for the CC Pay), In Mixed payment, create new payment using Bank CC Pay, report the payment for that invoice. If you need to report any CC processing fees, you can do this as well in the mixed payment.  

The reason for the CC Pay, is because it’s common that the payment (cash) does not flow directly to the traditional cash account.  By using a separate cash account (bank account) you can better control the posting when needed. 

Best regards, 

Thomas