Now, I don't know how this floating Z-axis works and if it's part of a THC system etc, hopefully Tom will jump in there. But if "home" for the Z-axis is where the tip touches the table/material and you really want to have your machine zero 3" above that point. Then enter -3 in the home offset. If you want it to automatically move up those 3 inches you'll have to edit the homing script, it's no big deal but lets not go into it before you know that is what you really want.
Having a floating home/machine zero like this seems awkward to me - but then again, I'm not used to how a plasma machine normally works so I may be way off - in which case I apologize.