Hey Ross,
I think you should in any case finally check the machine for rectangularity by milling something. If you program a simple rectangle as a toolpath, nearly as big as the workarea, and mill it with the tip of a V-bit, you can then check if the machine produces right angles or not, by comparing the diagonals of the grooves you milled, e.g. with a bar gauge.
See Homing vs. Zeroing.
Homing is done once after startup of the machine. It allows the machine to be sure where its carriages are by first driving them home once.
Zeroing XYZ means telling the machine where the workpiece zero coordinate of your 3D model is to be found on the real workpiece. It allows the g-code toolpath which you created with your CAM software to start at the correct position on the workpiece.
Zeroing Z alone has to be repeated everytime that you changed a bit, since bits have different lenghts and the machine needs you zeroing the new bit to ensure it will start to mill at the right height on the workpiece.
Here the manufacturers support videos: