cutting into bed right now...have a quick question!!!!

ok, so i am trimming tubs to fit into the bed...we are smoothing a chevy fullsize bed...anyways, if we are smoothing the bedside, do i need to cut the tubs so they butt up to the factory sides and then cut the sides to fit around that, or do i leave them flat and then bring the flat pieces up to the edges of the tub?