Can I assume this is an AA ticket and AA flight number on AA metal? If so, then I'd rely on AA. However, I had something similar happen where I ticketed a a flight on BA recently, with a BA flight number on AA ticket stock. I chose my seats on BA.com and the seats then registered under my reservation on AA.com. However, BA moved me (not sure why, someone who outranked me probably wanted the seat, and the one I got is actually probably better), and it shows up that way on BA.com, but AA.com still has my original seat.

Can you change the seats on AA.com? If so, then just use that, since AA is the final authority on where you'll sit anyways.

Oh, and if you are a status holder on AA you'll want to get seats through them anyways (assuming you're flying coach).