Tips for double sided PCBs


I'd like to mill a two-sided PCB and I'm looking for suggestions on a good way to do this.  On my ShapeOko I have a piece of masonite attached to my waste board (via double stick tape).  I milled the masonite flat and milled in a left shoulder and bottom shoulder to register the PCB.  For milling two sided PCBs I'd like to do something along the lines where there are some registration holes drilled in the masonite.  I'd attach the PCB to the masonite and run a program that would just drill the registration holes in the PCB.  Then I'd use one set of holes when milling the bottom.  Then flip the PCB over so it's in the same general area as before then line it up with the other set of registration holes.  I don't want to do the scenario where I flip the PCB over so that the right edge when milling the bottom is in the same spot as the left edge when milling the top (or something like that).  I hope I'm making myself clear. 

Once the bottom was milled, I'd go to 0,0,0 on the workpiece coordinates, them move the machine a specific distance along the X-axis the reset my  zero then the top.