Hi! The output from the Vectric programs is written in gcode, and describes where the cutter should move, step-by-step through the cut. It uses physical positions in mm or inches. The output from the Vectric programs is read in by the controller software, and it makes the conversion between position and steps of the motion system. I use Mach3 as a controller, but there are many options for the home builder. These controllers are configured for each axis, and there is no need for X, Y or Z to have the same calibration factors.
You should sign up at the CNCZone forum ... it is well-read by machine builders, and they can offer lots of advice.
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