Ok, just to be clear what you are meaning, if you home the machine then jog to where you want zero to be in G54 then zero each axis DRO that will mean you have just set the G54 offset (its the default) You then can close Mach and it will ask if you wish to save the fixture offset, you click OK and next time you start Mach you home and then if you command a move to zero it should go to the previously saved position.
Is that not happening?
Hood