Quite clearly, the thing you need to do is set the 0.0 position of your plasma program and align the plate with the X or Y axis. I do not see the purpose of the two reference holes on the plate unless you are going to do multiples of the cutting. In that case you need to make some sort of jig on your table to hold the plate, with some sort of indent (or outdent) for the holes, so that subsequent plates locate in the same place.
If you know the relationship between the holes and the rest of your program, the laser probe is irrelevant. In this case a drill bit, or rod of the same sixe as the hole will suffice. Zero your table if you have lhome switches, put the drill or rod in the chuck and move the table , until the the drill bit or rod slides smoothly into the hole. If the holes are semi-circular, move the table to the correct position and put the plate in place against the rod.
The alternative is with a drill and two short pieces of rod, drill your table in the correct place for the holes, and the two pieces of rod will tap into the holes. All you plates will then fit in exactly the same position on your table.