I have been considering different types of jigs for 2 sided machining. This is what I have come up with so far. It is similar to something I had seen on a shop bot video. The only difference is his jig was a box and he hammered a wedge in to hold the work piece.
That will work fine so long as the material you are working with is square and your fixture is square. The other way to do it is with 3 dowel pins in holes in your waste board that are at 90 degrees. 2 on the long axis of your material and 1 on the short axis just a short distance up from the long axis holes.
Also remember that your X0 and Y0 will move when your flip your work so take that into account for the second side.
Dave
Yep, I forgot to flip image on the screen once, ended up having two box shelves up, other two down. My wife was laughing me saying, your box is for two way use, if you want to use other two shelves, you have to flip your box over. 
I typically like to flip and align my part through a center line and dowel pins. Most reliable setup in my opinion for lining up both sides symmetrically.
Are you guys just getting wooden dowels and sticking them in the predrilled holes in the wasteboard? Or are you drilling new holes?
It would be better to have the machine cut new holes to ensure that they are square to the spindle. The wasteboard is probably close but I wouldn’t trust it.
