I see. Then can a player, whose ship stops at a settlement (i.e. it does not have any moving points left), load the tokens on the ship so that the settlement can store more tokens?
Why not? Have you found anything in the rules which prohibit this?
Also how does one show that the tokens belong to the ship and not the settlement?
Just place the tokens either beside the settlement or the ship in a way which shows the other players that they belong to the settlement or ship.
Dr. Reiner Düren