Here's how I have done it in the past...
Chuck/mount to faceplate, rough center and machine SIDE of wheel flat.
Remount wheel using flat side to register and face second SIDE.
While still mounted, drill, bore and, if needed, ream center hole.
Mount wheel on suitable arbor and turn wheel circumference, guaranteeing that rim will run true when wheel is mounted to engine. [Nobody likes to see a wobbly flywheel.]