Lower your z-axis until the bit is .01" above the table top surface and zero it with the (ZZ) command. Checking the distance between the table top and your router bit with an automotive feeler gauge is one way to do this; a zeroing plate and the zzero.sbp program that comes with your ShopBot software is probably the best. Since I use a vacuum to hold the plywood to my ShopBot, the cutting files leave .02" of plywood uncut at the bottom of each cut so that the suction isn't lost. After each sheet is finished cutting I slide it off of the ShopBot and cut the rest of the way through with a utility knife.
Raise the z-axis up enough to clear the sheet of plywood and put one of the 4mm plywood sheets on the table. Make sure that the corner of the sheet is over the 0,0 point of the table top. Sometimes imported plywood will be a little bit wider or a little bit longer than 4'x 8'; as long as it fits on your table and the edges line up correctly on the table top, the larger sizes doesn't matter
Using the Z2 command, zero the x and y axis when the center of the bit it over the front left corner of the plywood (the 0,0 point for a ShopBot). To double-check this setting, make an (MX,-.125) move and see if the front cutting edge of the router bit is flush with the edge of the plywood. If it isn't, move the X-axis back or forth until it is flush, then reset your axis with the (VA,-.125,) command. Even though it's not as critical, when your done repeat these steps for the Y-axis.
