Could someone explain what Safe Z is, what it does, and where should it be set?

Safe Z, means just what it sounds like. It is a position to which the Z axis is retracted, which will not crash the tool into anything. This is usually just below the home/limit switch of the Z. In the menu, you can set the Safe Z position relative to Home 0.000, or a distance in units just below the home. I set mine to .050" below home. Also, you can set the action for the machine to go to Safe Z if you hit the stop button.

Thanks for clearing that up for me.