I always set the material thickness in the software to as close as I can get it to the actual thickness of the material. It just give me a good base to start from. Then other adjustments are much simpler. I don't know what control software you are using but most have a command line. After zeroing the bit to the spoilboard type "Z0" on the command line, or the equivalent command for your control software, and see if the bit just touches the spoilboard. If it does, then at least that portion of the setup is correct.
When using a cut that goes all the way through the material I just use "Z=" to set the depth to the thickness of the material. the machine always leaves about .001" skin. That almost always works for me. Even if it cuts into the spoilboard a little then "oh well". After all, it is a spoilboard.