I just spoke with another AA award agent. I was told they can combine award travel and paid travel in a single PNR. However, she did mention that it would be two different ticket numbers.

Another option that was suggested was to book the AS flight on the AA website and that way if anything happens with the AS flight I only have to contact AA to rebook all the flights (even though there would be two PNRs and two carriers involved). EDIT - I checked this option but I can't get a setmap to show for AS prior to having to hit the purchase button, also says its on a Request basis (doesn't sound as smooth as getting it directly from the AS website).