If you elect to charge a convenience fee on electronic payments, there are various ways the Customer gets charged this fee. If you haven't yet set up your convenience fee, check out this support article that shows you how.
The following is an example of how the Convenience Fee can be set up:

In our example, there is no charge for ACH payments, but for EACH credit card transaction; there is a 1.5% fee. So for $100, the fee would be $1.50.
Customers are charged the convenience fee in the following ways:
Automatically each time a payment is made on the Enroll Form
Automatically each time a Customer pays through the Customer Portal
Automatically each time an Auto-Pay event occurs
Manually by an Administrator each time they enter a manual Tuition Charge on an Account. For example, if an Admin User enters a $200 Tuition Charge on a Customer's Account, then the Admin must manually put in the $3.00 convenience fee.