What you do depends on a lot of things:
What kind of paint are you using? Some have no hiding ability at all.
What do you want to achieve as a final result? Perfect finish or just all one color is fine?
The type of filler depends on the paint - use something that's compatible.
Polyester filler is easier to work with than epoxy. Goes off faster, sands easier. Polyester is what the boat's made of.
To achieve the perfect finish, you'd go over the whole boat with a fairing compound (3M Premium Filler)
Sand the whole thing perfectly smooth, then paint - 2 part polyurethanes (Interthane) work really well, are really hard and tough but a little tricky to work with. Best to have a dust-free place indoors to do the painting so that stuff doesn't land in the finish and ruin the gloss.