Same Problem
I first visited "manage bookings" on the Qantas site to get AA record locator from the BA booking code, make sure that the tickets were passed over to the AA computers (doesn't always happen without some help), and insert AAdvantage numbers. We actually had 3 separate PNRs. Was able to get seats for the first/business booking, but not for the 2 coach. We have one Platinum passenger in first/coach and one Platinum passenger in coach.
I am concerned about overbooking, getting the Platinum free bags, and getting our TSA pre-check.
Last month we could not use kiosks for boarding passes and had to go to the counter when flying with Avios on AA.