i mainly run mazdapseed6's or LTCR's so i have my body posts cut fairly short. And what i do is roughly trim the body to height then lay the body on top of the mounts then line up where you will want your wheel wells to be, then from underneath use a flashlight to create a shadow of the body post's on the body and mark them on the top side with a marker. Once you have reemed the post holes Then i mark the center's of the wheels and use a circle cutter for the wheel wells.
A good trick to get the proper height of the bottom edge of your body is to run a standard sharpee on it's side along your setup board marking the side of the body while it's on the car. Doing this will give you i think roughly 5-6mm clearance.
It's quick and easy