I had the opposite issue--I booked through AA and had flights on both. I was only able to select the AA seat. However, AA sent me two numbers, the PNR for AA and the one for QR, which let me look it up on QR's site. I did end up having to call QR for my seat, as you will likely have to do with AA. I was only able to select/change seats after check in on QR. I was in Business/First on both flights too, but AA will do it over the phone, just as QR did. I did get both numbers, though, and was both surprised and pleased to do so. It made things much simpler for me.