Disclaimer: We are in implementation stage and this idea is based on what we have seen in the demo.
Currently the payment made by parent is applied to the oldest charge. The billing clerk has the ability to choose to apply payment but the parents don't. If the parent is paying for a particular charge (eg. Transportation) but there is an older fee (eg. Tech) outstanding, the amount is applied to Tech fee instead of Transportation and the parents see that Transportation fees due event though they paid for it. To avoid confusion and disputes, the parents should be able to see and select the charges they are paying.