I drilled the holes for the FCS plugs after shaping and sanding but before glassing ...apparently i was supposed to drill the holes after the board was glassed and hot coated.
You can still sand the plugs down and glass over them. It's more difficult but certainly can be done.
I recommend glassing a small later of glass over the holes first and re-drilling or cutting the fiberglass with a razor blade. This will protect the foam when sanding the plugs flat.
Put a piece a masking tape over the slot and screw holes before laminating.
After the hotcoat has cured you'll have to cut through the resin and remove the tape.