Unless I'm mistaken, yep, the boats run on a track. That's why the water is the color it is.... so you can't see the track, that and of course it makes for better jungle water.
I'm sure the skippers have other duties besides running through the spiel and shooting hippos and whatnot, things I would think would be expected such as cleaning up their boat or turning over lost articles to lost and found or whatever, just like most of the Disney CM's, but what else exactly they have to do I wouldn't really be able to tell you.
Upcoming Trips to WDW:
Dec 6-10: Disney Wonder
Dec 10-19: Port Orleans French Quarter