I was a little confused too... When I called, I told them that I had originally booked a room for 4 nights at the discounted AP rate. I asked if I could make a reservation using the book 3 get 2 free promotion and the CM said that AP holders can book room only "packages" and get the perks that come along with it (early entry for Toon Town, priority seating vouchers for DCA, lanyards w/pin, downtown disney fun card). I had to give our AP #'s. But, instead of only paying a one night deposit and pay the balance at check out your "package" must be paid for 30 days prior to arrival.
I hope this helps...