Just stand there. The boat moves suddenly (I didn't see it happen), as I think someone already mentioned / illustrated. Looks like it moved to a position ready for transport, perhaps. I tried jumping into it. That, big surprise, didn't do anything at all.
edit: I was asked "do you want to use The Skill", I think, or words to that effect, more or less. Upon flicking the switch, that is. My character responded with "Yes".