You wait until the Alaska flight got closed.
This does usually happen some time while you're already taxiing to the runway.or have just taken off.

Afterwards FJ's online check-in should let you check-in.

​​​​​​If this won't be the case: if there's enough time you can go to FJ's check-in desk @ TBIT or you proceed to the gate and let the gate agent take care of you.