I got a PM from one of the travel agents on here that answered this and more after I posted, this is from my notes: (Sorry to the person that gave me all the info, I deleted the PM so I can't credit you!)
The room only and package system are different. If you book a package after a room they cancel your room and rebook. A base package, which is room plus tickets, you would pay for 45 days out. You could add dining and ticket up until 3 days in advance and pay when you upgrade. The only exception to this would be if a promo comes out you want to take advantage of, than you would have to follow the regular booking guidelines.
If a promo comes out, you can call to see if it can be applied to your reservation. If it there are rooms left at that rate, they will apply it, but there are only a certain number at each resort for each promotion. So, just because you have a room doesn't guarantee you can get the promo rate.
Same thing for AAA rate, only a certain number of rooms at that rate.
If you have a room and don't get the discount you want, you can ask if there are AAA discount rooms available and AAA can take over the reservation. The AAA agent can take over your reservations and you don't lose deposits or anything. Some kind of 'transfer form'.
If the
Travel Agent that PM'd me is out there, maybe he can elaborate/correct anything I missed.