Those numbers are not in the range they were designed for. Top of Material is only needed if Ohmic is turned Off, you would then jog the Z axis down till it is touching the material and press Set next to Top of Material, the value would be a negative number. You would then jog up 2 or 3 inches off the plate and press Set next to Partial Retract Position again would be a negative number. With the Z at the top of its travel Machine Position will read Zero, if not then you can Press Reset Z to set it to Zero from there all movements in the down direction is negative travel.
Once you have Reset the Z position at the top and if you then jog the Z down to either set your partial retract or top of material or just want the torch closer to the material to better find a Program Zero location, to raise the Z up press Set Program Zero then press Go to Program Zero and this will raise the Z up to its upper most position.