I don't really have any answers, but some educated guesses based on AY-operated AA/BA-codeshares I've been on. I'd say you will encounter a whole lot of problems ranging from lounge access to points accrual but if you call AY customer service and are persistent, they will be able to help you with at least the following:
- AY booking reference
- seat reservations (probably your AY status won't be of any help here pricewise or seatwise)
- meal preorders in J

With the AY booking reference, you might even be able to pick seats and meals on AY MMB, but then again you might not (it could show you a seat map full of "taken" seats).