1. Open the Payment that appears with the incorrect amount.
2. Select the Student Billing Details tab
3. Increase the "Apply This Amount" columns for any row so that the total of all rows equal the total amount of the payment
4. Alternatively, you can add another row where "Reduces the balance of" is set to the payer and "Transactions For" is any of the valid choices.  On this row, add the remaining amount that is need to fully distribute the payment