The current setup of the payment plan seems to be intrinsically broken, because it was set up so the (single) payment plan controls all, when a payment plan should be subordinate to transaction records.
Instead of having transactions (specifically FA credits and school fee charges) associated with one payment plan, transactions should have a payment plan associated with them, allowing for each transaction to have its own, possibly different, payment plan.
Yes, this might mean a family is billed at different times for different plans, but sometimes this is what they want!
This would also force itemizing how much of each charge is due on statements (instead of just showing a lump sum due), but this would only improve transparency (and family comprehension of what they are paying for), and make it much easier to reverse/adjust individual charges during the school year.
It might be necessary to add a new panel, similar to how FA has its' own panel; a separate area to show charges on payment plans, and include the individual installments as charges in the transaction view, just as FA credits are currently displayed.
Find someone who remembers how Student Billing worked, and pick their brains!