Try the code from the estlcam post, That might explain everything much better than I am. http://www.vicious1.com/estlcam-basics/
They are not normally closed, not in my firmware. You might have wired them that way but that is why I don’t suggest starting with them, too complicated for a first timer. Just unplug them and start as suggested.
Setting the Z is very easy, for milling usually you mill off the whole surface so precision isn’t very important, but still it is easy to get with a spinning tool. A bit tougher with 3D printing but it is simple, you can adjust it while it is making the outline.
Give it a try first.