With the engine mount out of the airplane. The back of the mount is the same as the firewall. now lay a ruler along side the mount with zero inches at the back of the mount, place your engine on the mount and mark where the engine should sit. do not attempt to mark the holes for the engine at this time. use the front of the flange the holes are in. Do both sides the same way.
now attach the mounts to the firewall, slide the engine onto the mounts use a small clamp to hold the engine in place and double check your measuements if ok mark your holes for the engine, if not ok adjust engine position double check then mark the holes for the engine. A nbr 2 pencil works good for marking
hope this doesn't confuse you... Good luck