There may be an easier way, but in case there isn't ...
I think (though I haven't checked it) that the game fills up the seats in a particular order. So, to ensure that your loon sits in the right one, you have to make sure that an appropriate number of other loons get in first. If there aren't enough soldiers in the squad, use gamelogics to make up the numbers.
To get the player into a particular seat is more tricky, since the game can't control what he does.