Run the machine to its physical limits and press the "Ref All Home" button. If the limit switches are not configured, Mach3 will reference the axes without moving them.
I don't remember whether the default Mach3 screen has individual "Ref" buttons for the axes. Haven't used the default screen in many years.
The Z axis normally has 0 at the bottom and a positive number at the top, but there is more then one way to skin a cat.