You can't just paint over the chips.  The paint on the board is in the gel coat.  the outer gel coat can and will chip off when it takes a hit.   It doesn't mean that the under coat of epoxy cracked.  Your board is most likely still water tight, but check to make sure the under coat of epoxy is not compromised.   The gel coat on these epoxy boards is brittle and easy to crack.  I've got  a few chips on mine just from laying it on the pavement or bumping a wall.  It doesn't spider like a PU board it just chips off.   When you patch it you can just use epoxy resin from a patch kit to smooth over the hole in the surface  and then paint it with an epoxy spray paint.  spray a few heavy layers of clear coat over the area to keep the paint from getting scraped off.    The last patch I did to my gel coat was over a year ago and it's held up great.