1.) if the paint is translucent or even semi, your fucked, your either gonna see scratches, or parts with wood filler in em. One rule about woodworking. you may not see it now, but as soon as you hit it with primer or a stain/clearcoat, its gonna stick out likea sore thumb.
2.) what grit are you using that you ended up with some decent scratches? If you want it to be smooth, follow this Grit-wise, 1000, 2000. Dont work too hard on the scratches trying to sand them out. Youll end up with some nasty divets.
3.) using filler primer may or may not work depending on how nasty the scratches are. If theyre dep gouges, no, it wont work. If theyre fine scratches left by individual grains in the paper, more than likely, yes.
Anyway you look at it, with defects in wood, its either fix though experience or learn.