I'm gonig to do the inserts and foam inlays as a seperate step so I can sand out any heigh spots. You can't sand it out after you glass it up without going into the finberglass. Every time you sand into the fiber you weeken the board. That being said the little dips and low spots will get filled with the hot coat and the primer coat and sanded out. It's what gives you that cool looking black and white brushed speckle on carbon fiber windsurfers and sups.
Not sure if I understand, but doing before layup will seal it better and will look cleaner. With my inserts I just counter sunk them flush into the AIREX core and set them in epoxy leaving a bulge remembering that the core material will suck up some of the epoxy while curing. Took my router and neatened up around the insert. Now the only weak point I have is a small 5mm hole where the screw/insert is. Doing it afterwards will leave the whole insert block at risk of separation for core unless that is you are laying up over that again?
If you worried about laying up over inserts and not being able to find them. Just make a template or depending on insert block material (?) you can magnetizing them and locate using iron fillings or use compressed air to cool general area down and you'll find them that way.