Customer Account is used when ever you need to keep track of the amount paid by a customer. For you to select Customer Account you must select a customer when processing the order so that the payment can be linked to the customer Account. The customer account could be used when you are processing a transaction on credit, signifying the customer would pay later or its possible the customer has credit balance(Advance or prepayment), you could select the customer account when validating so that the advanced payment could be applied to the order.