Ive had this come up alot lately. The Falcon is larger then the base.if i have a fighter im trying to get in close and the ships are touching but not the bases can i leave my ship off and finish the move

Most people play it like that in casual games.

In tournament games, there's a rule that you must always properly represent your ships on their bases. You should bring along extra pegs so that you can adjust the ship's height during a game. I would suspect that this rule is easily (and probably sensibly) overlooked for most tournament situations. As soon as the ships part ways, it's easy enough to replace them on their bases again.

^

This. Exactly.