No, actually for AA coded JAL flights you need to start the check in process on aa.com: Within the check in window of the flight (24hrs?), you will see a check-in button on the manage my booking webpage and clicking it would take you to JAL to finalize check-in. If you want to secure a seat before check-in, you need to call AA and have them select seats for you (JAL wouldn't help). Notice that some of the lowest fares wouldn't allow seat selections in advance