It's a good idea to get the stringer flush with the foam so the fiberglass lays flat across the stringer. If it is not flat there will be a gap and there's a good chance the glass will crack there letting water into the board. Also, a smooth, clean shape is easier to sand. Wavey rails, high and low spots on the deck and bottom will cause a lot more work sanding.Take your time to get the shape as nice a possible (without overshaping) and you'll find the glassing and sanding process will go pretty smoothly.