When you upgrade tickets from a package after check-in (whether it's to an AP, adding days or just adding a park hopper option), it's on a per-ticket basis. The key is to do it *after* you check-in and get your room key. Go to the Lobby Concierge desk and they should be able to do it. (though perhaps not the upgrade-to-AP option)
(This is how people with APs were doing the Free Dining promo last year if some in their group didn't have APs. They'd book the trip with 1-day base tickets for everyone, and then after check-in they'd upgrade the tickets of those who needed more days.)
-Rob