You can, of course, still use inches or mm. G20 makes the machine move in inches, G21 makes the machine move in millimeters.If you include these two commands in your programs, Mach will move in either. It will take all your settings and convert them to the other unit.
The only thing the set up units means is that ALL you settings, motors, tool offsets, general offsets etc etc must be in your selected unit - i.e. MM.