Zero 3 axis .... one way
Not quite sure what you want to do, but one way is to use two hold-downs to secure the work piece / say on the upper left side. A third clamp holds down the Zero plate on top of the work piece / with the aluminum edges parallel to the work piece edges.
Zero to the top or the plate, and then drive/ nudge the Bot around with a 1/4 inch bit so you touch the edges of the plate from the x & y directions .... when the bit touches the edge of the plate set the proper read out to -.125
The 0,0 position should then be over the lower right corner of the material. Remove the plate and re-clamp as needed.
The decimal point seems to be the most important on the z axis... x & y not so much....
ShopBot... Where even the scraps and things you mess up and throw away are cool....