In my experience (also as a first time builder) any hole/dimple no matter how small ends up staying a hole after coating with epoxy.  I decided I'd just live with the imperfections and didn't bother sanding obsessively.  Alternatively, you could 'fair' the fillets with thickened epoxy (I did a bit of that around the skeg) though I'm not sure the effort is worth it...

Mihai

I am currently trying to finish my Annapolis Wherry and my experience is that the little dimpling won't always go away.  If you sand too much you will just have to do it over.  (I know I did it, and had to apply more fillit).  I think there are things we will have to accept and others we can have control of, these dimple are there and we will be best to live with them.

This is probably too late - but apply a thin over-coat of epoxy.  Blend it in the best you can then wait about an hour.  Use alcohol as a wettng agent to blend in the epoxy even more.

I did not do this but the 5 coats of spar varnish did fill in the holes.  GOOD LUCK

You said, "prior to adding the "two thick coats of epoxy...".  My suggestion is to not add "thick" coats of epoxy.  Make the coats as thin as you can get them, using a plastic epoxy spreader to get it as thin as possible then tipping out with a foam brush where necessary.  You can always add multiple coats of epoxy to make it as thick as you desire but if you put it on thick it will be impossible to stop the runs and puddles that the epoxy slowly forms before cure.  This is the voice of experience.  I'm still sanding.

Many of the dimples might be tiny bubbles in the fillet that become exposed by sanding, so just continuing to sand might never get rid of them. If you want a super smooth fillet for aesthetic reasons, you will probably need to fill the tiny craters with a light application of somewhat thickened epoxy. Then a careful sanding before coating with thin coats of unthickened epoxy should produce the smoothness that you want.

Grant