I think you'll find that for something like your talking about, (1/16" nicks, scratches) get a small artist brush and carefully touch up the spots with no filler. Gelcoat is fairly thick. Let it cure for a few days before sanding. The stuff shrinks alot. So if you sand right away you'll find yourself filling and sanding on and on.

Bondo and such has a more pourous surface and is normaly used to fill larger areas. Glazing putty has a finer filler and is used to go over "Bondo" before priming. Glazing putty is the right stuff for smaller scratches.