Setting Extruder to Bed Clearance on a Wilson II Printer

Still working with Z-axis Issue. Question on Z-axis offsets…
There is an option on the machine console that allows me to
set a Z-axis offset. There is a G-Code option that allows
me to set a Z-axis offset and there is an OPTION in
the MARLIN code to set a Z-axis offset. Question of the
Day: Which has the final “say” on the offset? Is the setting
made on the control panel, the MARLIN code, or the print
file G-Code??? In my current configuration they all three
have values and, of course they are all different!! ??
Any advice anyone??