SkyTrip, welcome to FlyerTalk! I assume that when you say that your AA and Qatar flights are not linked that you mean they are not on the same ticket.
If you could clarify, that could get you the best information. In any case, I'm going to move this to the forum dedicated to discussing American Airlines, as your question concerns AA's ability to give you a Qatar boarding pass. Ocn Vw 1K, Moderator.