To make the cutout mark for these wheelwells, hold them up in place where you want them height-wise. I usually keep the bottom flange of the wheelwell 3⁄4 inch below the edge pieces the bed wood fits under. If you keep the flange down it will be under the bed wood. If you put the flange up with the stock edge flange that will work well too, except the wood will have to be specially routed to fit. Not hard, just creating extra steps. If you are planning on raising the bed floor for more rearend clearance anyway then it doesn’t matter.