CaptRR,
OK, as your using Eagle and the pcbgcode ulp, It generates the Gcode (assuming your using the right profile) to dump directly into mach. No need to run it through anything else to get it to run.
Alignment,
OK, I use a fixture that holds the raw board in one place. I use G54 as the top side and the origin is located at the lower left corner of the board. When I flip the board over, the same origin point is now at the lower right hand corner of the board and I am in G55 fixture mode. In order to do this, I have customized the post processor files in the ulp to accommodate this.
What I have done is made a pocket in a piece of derlin and used this with a vacuum pump to hold the board flat. I also use "autoleveling" software to accommodate the imperfections of the pcb.
Art
AKA Country Bubba (Older Than Dirt)