fairing compound

Does fairing compound go under the glass/epoxy?  I have a few defects in the panels of the hull and was going to paint the hull anyway, as this is my first build, I was wondering if I can use the fairing compound right on the bare wood and epoxy/glass over that?

You can, but it's more usual to put it on over the glass. In fact, when painting, it's used to fill the weave and fair the hull.

Laszlo