allocating bank charges on CP

Hi, I have a customer payment which includes a bank charge, the customer pays "X" amount, "Y" is deducted when it hits our bank. Each payment is short the "Y" amount which is a bank charge. Previously the person I took over from was putting on the payment for the "X" amount and then putting the "Y" amount in as a separate supplier payment of a bank charge so the bank amount would balance. Is there a better way to do this? I want the bank charge to be linked to the customer payment, the customer should in theory be paying extra to cover the charges, and in theory the amount that reaches our bank should be entered onto their account and the balance left owed.