I haven't used this much, but what I have used worked well. I'll try to help.
First, I took the shortest tool (or empty holder) and touched it on anything near the full stroke of the Z- and with tool 1 selected, make that Tool 1, Z zero.
Then put all the other tools in on at a time , select the appropriate tool #, jog to touch and hit Set Tool Offset.
Do this for every tool, they will all be offset from the empty Zero tool #1 and all offsets will be positive, meaning that the Z will need to be more positive for the longer tools as they are referenced from the shortest tool with the Z fully extended.
Then, you can put any tool in that you want, make sure that the correct tool is displayed in the DRO, touch that tool and Zero the z and all others are then in reference and ready to go.
I hope I said that right, as it worked like a charm here before.
HTH,
Russ