I've just had a look at a BA reward booking I have on Qantas. On BA.com it won't let me edit the FF numbers and the same when I log into Qantas.com, so I'm guessing it's the same for AA now.
Not familiar with the AA regs of late, but do you have to have the AA FF number in the booking to get the benefits of free bags etc or can you just show it at check in?