I think the answer is "it depends".
The only definite thing that I would know to say is this -- If you book a Room-Only ressie with a
AAA discount -- you would NOT be able to put an additional room discount on top of that. For example, if there is an AP room discount or a General Public room discount, then you can not get either of those discounts in addition to the AAA room discount. You would need to figure out which one is the best deal for you -- and THEN you have to see whether the desired discount is still available for your resort and your dates. Don't give up your AAA discounted ressie until you know for sure about the availability of a better discount.
FYI -- You CAN book a AAA room-only discount through Disney or through DU. You do not have to go through a AAA rep. However, a AAA package must be booked through a AAA rep.
In general, though, you do have more flexibility to mix-and-match discounts when you book "a la carte"; i.e., no package.
Other deals, such as the one that you mention -- upgrading your tickets if you have booked through AAA -- you just have to read the fine-print (or have the rep to interpret for you!). It sounds like that deal would not be available to you if you have booked your room directly through Disney or DU.
