This question is more for understanding everything along with the terms.
In the Machine setup, what is the Cut Depth? Is this how far into the material it will cut? Because it asks the material thickness and it also asks for the Z increment. So I'm guessing its asking for the cut depth per run? So if the material is 1 inch thick, you could tell it a cut depth of 1/4 inch... but why ask the Z increment?
I'm a little lost
Cut depth is the final depth of cut. Z increment is the depth of cut per pass. For instance if you wanted to cut a slot 1" deep in four passes you would specify a Z increment of 1/4". If you are cutting something out of sheet you may want the last pass to be quite shallow so the part doesn't move. Say for instance you are cutting 1/2" MDF with a 1/4" cutter and you want the last pass to be 0.05" deep. You could set the Z increment to 0.225". This would then make 2 passes of 0.225" plus one pass of 0.05".
By the way, have you found the tutorials? If not, have a look in Help->Tutorials.