What grit are you sanding off the rattle can paint ? I wouldn't go any heavier than 80. Are you truly getting into the glass...or are you just into the gel coat...(ie got any glass hairs sticking up ?)? The top side repair of this is the same either way. Mix your epoxy resin & hardener with some West Systems filling and fairing additive (available at your boating supply houses...Eastern Marine etc.) and brush it on the damaged spots...build it up as necessary. If you've gotten into the glass and the spot is weakened...before you attack the top side... flip over the top, run a grinder with some 36 grit in the bad area, get some fiberglass matt, cut it to size, lay it on some saran wrap,mix up the epoxy & harderner, paint it on the repair area, paint it on/infuse it into the matt on the plastic wrap, pick up the plastic wrap/matt and slap it on the repair area. After you get it situated and pressed on and if need be rolled out, just carefully peel of the plastic so as not to lift the matt off and let her set up.
A couple of things, even with the filling and fairing additive, your top side repair will be harder that the surrounding gel goat....sand carefully. Also, there comes a point of diminishing returns, on one of my tops I had @ 25% of it painted with the filling and fairing epoxy....much more than that I may consider an alternative approach. Not that I don't love sanding and sanding and sanding.....
Finally, after you've done your repairs and have the whole thing with scratches no bigger than 80 grit, I'd lay down 3 coats of PPG Omni High Build primer and block the whole thing out by hand with 180 (this will even take care of most of the "factory" pinholes). If after you blocked it all out you have decent primer left (ie you haven't gone through it all in multiple locations), final sand with your DA with 220, or by hand with 400. If you've gone though everywhere, hit it with 2 quick coats of primer and then final sand. Blow it off real good, wash it down with prep solv, tack it and shoot with your PPG. If however, you use someone elses primer (other than PPG/Omni)...use their color. My 02 and what I've done on two of my tops.