The Z setting comes into its own if you have repeatable tool holders (I have TTS). You can premeasure your tools and 3D probe. I do this off line using a toolsetter and a tiny granite plate from Tormach. It has a hole in it for the TTS holders so they sit flat on the plate.
Using QTdragon, you probe for the surface with tool 99 which holds the probe.
Then you can do a tool change to your desired tool and Z0 will be the surface of your workpiece.
This lets you generate a single gcode file for all tools, whereas my mate runs out gcode for every tool seperately and touches off as you would on a manual mill each time,