Those screw holes ....First, make the wood surface smooth and free of loose stuff, e.g. take the screws back out after the 2 layers are cured together, then remove any wood splinters, glass, etc. Then I sweep, then shopvac each screw hole. I fill the holes with epoxy that's thickened with fairing compound (phenolic microballons or glass microballoons plus silica). I fill the holes to the point that there is a 'bump' of epoxy above flush. Trying to scrape off excess creates a dent over the screw hole that has to be filled again later. If you leave the fill epoxy bumped up above the surface, then you can scrape it flush with a carbide scraper after it's cured. I find that this method results in a smoother, nicer, surface. It's how I fill all screw holes...
You'll want to fill on the inside and outside. The inside of the hull is already glassed at this point, and that's fine. Just fill, cure, scrape as described and put a finish coat or two of epoxy over the filled holes and call it good. On the outside, it'll all get glassed over when you glass the bottom assembly.
Brian