So I am using the (RepRapDiscount_Full_Graphic_Smart_Controller) LCD as an interface to the machine and it has a HOME Z option. Do I use that to touch off Z with the touch plate after homing x and y. Also, then I wonder if I have Z running the wrong direction so that when I see it drop Z slightly at the end of the xy homing it should rather be raising Z slightly at the end of the xy homing.
John
You never home the MPCNC Z axis. The touch probe lets your machine know where the reference surface is, the table or your material, whatever you choose in the cam software.
The LCD has a Home Z because it is set up for a 3D printer, do not use “home all” or “home Z”.
The standard workflow from the milling basics page is to home your X and Y axis (mostly to use auto square and for job repeatability), then drive to your starting position (usually the material corner or center), then start your CAM provided Gcode. That Gcode with then set the Current position to XY = 0, then it will probe Z to see where the reference surface is and set the distance accordingly. From there the job starts.