If you don't have good Home switches then the next best thing is to run the machine into some hard stops and call this machine Zero. Then from this you can accurately get back to any point on the machine and equally find any point in G-code by using the run from here in Mach3.

Working from a hole or mark on the machine isn't accurate enough IMO and the only sure way is thru either repeatabile home switches or pyhsical hard stops.