My experience is that having my AAdvantage number in the BA booking (I'm making an assumption that this will be booked on BA.com, but that could be incorrect), I can choose seats on the BA flights there. Then, I see the AA flights (even though booked on BA.com) on AA.com as well (and here is shows it as the AA flight number even though it's really booked with the BA number) and I can choose seats there.
Cheers.
Update: Tickets booked on BA. Was able to chose seats on all flights due to AA platinum status at no charge. (Now I just need a window seat to open up on the 747 in premium economy
)
No ability to request upgrade on US domestic AA segment as it was marked as a BA flight number. But I could still pick MCE.