You will need to check in at the JAL counter, your boarding pass will show the AA Code Share flight number on it but will be issued by JAL.

Be aware that JAL does not always allow advance seating with the Codeshares, sometimes they state that the Codeshare pricing does not include advance seating, so you could be taking the risk of flying in a middle seat.

Even with my status, I was unable to get advance seating for my AA codeshare flight on JAL.

If your concerned about mileage posting, it posts in the same time frame as normal AA flights.

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AA member since 1981.