When I booked JAL through AA, I was able to select seats by phone with AA, but JAL had no record of any of them. I was still able to get aisles on all but one however. This was some time ago, and I don't think JAL even had online checkin yet. But I found that out of NRT, many local passengers did not book seats in advance and most were assigned at the airport. So upon checkin at HKG, you may have some luck.