You'll get more answers to this question on the Codes board (under Resorts). But the simple answer is this--
Room only you can book through Disney. If you want a package (with room, tickets, and perhaps dining), you must book through an AAA agent. You get a discount off the room portion of the package, and that portion can vary from 10-20% off the room portion of the package. For us, it's about $400 off 8 nights at the Polynesian in August, so the savings can be significant.
If you book a package through AAA, you also get a few perks like preferred parking at the parks, discount on shopping on DTD, and AAA Storytime in the MK.