You can do anything you want to do as long as the location satisfies your set up. For example, you could use a shoulder bolt in one of the holes, drill and ream a hole somewhere and put a pin in it, drill and ream a hole for a taper ended locating ball , use scribed lines on the plate. Depends on how accurately you want the reference point or reference lines to be relative to what ever your going to mount on the plate.
If you made one yourself maybe align the holes with the X & Y axis and machine the sides.
Whatever works for you on it's intended use.
RICH