When you use Due Dates, by default the system will apply payments to the oldest due items first.
You can change this and let parents pick what they are paying for by going to More > Settings and clicking "Portal Settings" in the left menu. Then choose the "Options" tab.
Check the box labeled "Let Parents pick what items to pay for," and Save Changes.
Now when a parent logs into the parent portal and goes to the "Pay Online" section, they can pick "Other."
Then they tell the system what they want to pay for each student by selecting the student, the fee to be paid, and the amount. The system lets them pick from fees that are not marked as paid and have a due date assigned to that specific charge.
The system shows them each item they are paying for along with the payment total. When they have added all of the items to be paid, they click "Next."
The payment is then applied to the selected items instead of automatically being applied to the oldest due item:

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