Never tried, but IF ist possible, it will go like this:
The two ships must be in the same plot. Select the Missile in theloade ship, Wake it up, click the "Load on ship button" - it should ask you on what ship you want to put it, if there are multiple possibilities.
This is the way you can move normal troops from one transport ship to another at sea. Not sure if it actually works with Missiles.
Otherwise - like pointed out before - you can't use the "rebase" mission to put the missile on a ship. The ship and missile must be in same plot (Harbor, Fort), then the missile can be loaded.