AA and BA use different reservation systems. You have one booking # from AA where all of your flights are listed, and it is the most important one for you. Then you will have one or two BA booking ref # (depending whether or not your flights were booked as prime or codeshare flights or a combination thereof). If you try to select a seat on aa.com it will take you to ba.com to the 'correct' (operational BA PNR). You should only select seats in the booking where the flight of your interest is listed as 'confirmed'. Yes, you can also choose a seat in the other PNR (where that flight is listed 'information only') but it won't do anything. Your selected seats are the seats pre-assigned in the PNR where the flight has a 'confirmed' status. Pre-assigning the seats in the other ('information only' PNR) won't actually take the seats and they will remain free.