Waxing every time you use the boat seems a bit excessive to me, I wax my ski's a couple of times a year. But I guess if you got the time why not? I would wax anything that's fiberglass or metal, so yes the deck, motor cover, bulk heads, etc.
FYI I use a liquid wax called Blue Ice, it works well and is very easy to apply and remove, and you can use it on anything, fiberglass, metal, vinyl, rubber. It ain't cheap and I wouldn't use it on oxidized surfaces.
Lou