Lengthy post about setting Z. Auto vs Manual
What is the best way to set your Z? Should you use manual or auto touch off? It simply depends on you. Here are a few ways for each.
First, lets look at auto. Sounds simple, right? Just let the machine do it for you. Well, not so fast. Most people think once the tool touches the touch pad, they are done. Oh no. You have to tell the machine how far above the table is the top of your material, including the spoilboard. Sounds simple enough. Well, it's not so simple. You need to add the thickness of the spoilboard and the material and enter that into the external shift Z on the offset screen. Good luck with that if don't have a perfectly flat spoilboard. So here is what typically is done. The operator usually measures from the table to the top of the spoilboard from the edge of the spoilboard. But the edge is not as low as a few inches in because the gasket sets in a little bit from the edge, so anything outside the gasket is not sucked down as hard as the inside. You can get very close, and maybe close enough using this method, but it can vary.

How about telling the machine where the top of the spoilboard is instead of the table, and then just put the material thickness in the external Z? I like this better. But you must tell the machine this value in parameter 3411 in the controller. And each time you fly cut you change the value. And each time you change the value, don't forget to touch off your tools or you'll be off.
Now manual touch off. Have external Z set to zero. Then run the bit down to the top of your material and use paper or just your eye to know where the top is. Then go to the offset screen, then the tool set screen and change the length geometry for the tool in the spindle. You will be very close for your depth of cuts.
Now my favorite way - use a Z setter. My tool setter is 2 inches tall, so I set the external Z to -2.0000. Then I run the bit down to the Z setter and I know when I touch it because it has a dial indicator. Using the MPG, I zero the bit on the top of the Z setter. I will be very very accurate every time. I just do a tool change and zero every bit or just the ones I want to.
This is super fast and I'm not trying to add my material and my spoilboard thicknesses together.