While I fully support your opinion that better documentation is needed, I am not quite sure this statement is accurate. When I turn on my machine and it asks for me to load a tool, I always put in my “zeroing” tool which is a smooth 1/8" diameter carbide blank, and let it go through the first BitSetter process. I move the gantry all the way to the back of the machine and load and secure my stock. I then go through the probing process with said “zeroing” blank to set my x/y/z zero. I load my cut file and select run file. After pressing start CM pulls the router to the front and asks me to install the first tool that the cut file uses. I remove the “zeroing” blank and install the neccessary tool and we are off to the races. If my next cut requires a different zero point, I press “load new tool” on the run screen and load the blank back in to go through the probing process with the next piece of stock. Very early on with my BitSetter I had one z depth miscut (user error of not using the load tool button) and since then have held myself to the workflow described above and haven’t had any issues.
I could totally be missing something and be completely wrong and somehow have gotten lucky. Maybe @WillAdams or @Julien can straighten me out.