I hope i am answering your question, The cnc machine works on and x,y,z coordinate system. If you look at my picture with the big gouge in it, the gouge is parallel to the y axis. Left or right of the gouge is the x axis, and z would be in and out or depth.
As far as the origin goes, in my process the origin is actually the corner of my base board or the board everything is mounted to. I find the corner of that base board and this becomes 0,0,0 (x,y,z) and every thing in my cad program is located in proximity of that corner. This give me a good physical point to locate to in the cnc machine.
Dude break out the software and model something up!