From my experience and understanding, if you book thru AA, then they own the record and can update the seat assignments. I believe what's happening is they make a request into the JL system, then if seat is available, then it assigns it based on status. For example, they do block certain seats for emerald (exit row, etc). JL won't help unless they ticketed it or it's their flight number - no codeshare.

For example, if I ticket thru AA, I generally check EF for seat availability, then call the AA exp and request the seats I want.

If I ticket thru JL, then I call JL to request them. They recognize I'm emerald and I usually get the seats I want.

I've never had an issue with this approach.

Hope this helps.

Cheers.