Prepayment is a payment made online on the website at the time of ordering/checking out, in advance of an order shipping (including for backorders).
Payment is any payment made that is not at the time of ordering, or any payment that is made through offline means - such as calling directly to make a payment.
On your accounting statement you will be able to see orders you've made in the past and the payment type associated with the order.
Please note that any prepayment orders that have a negative balance "-" means that products that were purchased have either not shipped yet, or are backordered. This balance will change as products are shipped out. A negative open balance means the customer is in a credit position, not in an "owing" position.