Usually you use CAM software to plan tool motions from a CAD model. This is then post processed into a G-code specific for the controller of the actual CNC machine you are using
- Roland post processor for the mill at Trolllabs, and Mach3 postprocessor for the machine upstairs.
- The "underplate" is a sacrifice board, and it is there to save the bed of the machine when you need to cut through things, and usually you need to.
- Vacuum is nice for clamping of plates, but screws can be as good an options many times.
- Reference point can be anywhere - the important thing is to give the machine the same reference as all G-code from the CAD / CAM model refer to.
I 'd suggest that those who are interested in learing cnc milling having a look at "this old tonys" videos on the topic. Or actually, even if you are not interested you should have a look. He makes some good and inspiring content.. :-)