Actually, I believe it depends on whether the RESERVATION was made online or by phone. Reservations made online through the WDW website have a different reservation number code, and other than initial deposit payment cannot be made in advance for online reservations. If the initial room-only reservation was made by phone, then yes payments can be made towards that reservation but you must call to do the payments as well.
This was true last spring...if they have changed the online reservation system since then it could be incorrect.