Joel,
I think you are confused between the terms Machine Zero ("Home" position) and Part/Program Zero (lower left hand corner of your work piece - wood). It's not your fault, the 'Go to Zero' button should be labeled 'Go to Part Zero'.
The 'Go to Zero' button in Mach 3 is used to move your router from the Home position to the lower left hand corner of your work piece. In other words, once you establish the Home position (Machine Zero), you and Mach 3 can find any other X and Y position on your table. Just move your router (X, Y) to the lower left hand corner of your work piece, lower the Z-Axis to the top of your board, and then just zero out the X, Y, and Z-Axis buttons in Mach3 (Main Screen).
Now, when you click the Go to Zero button, Mach 3 will automatically move your router from the Home position to your Part/Program location.
Try the following: Turn off your Homing switch in Mach 3 for this example.
1. Move your machine (tool bit) to a random location on your table and call it "Home" (Machine Zero). This is usually located somewhere near the lower left hand corner of your table. Mark the location with an X.
2. Raise the Z-Axis upwards and stop at a point (just before hitting the Limit Switch) you want to call Home for the Z-Axis.
3. In Mach 3, click the 'Ref all Home' button (all zeros). You have now established the Home position for the X, Y, and Z-Axes. (Remember to Save your settings before closing out of Mach 3.)
4. Now, starting at the Home position, move the router to the lower left hand corner of your work piece. Lower the Z-Axis to the top of your piece of wood. Go to the main screen in Mach 3 and "zero" out the X, Y, and Z-Axes.
5. Return to the Home Position by entering G91 G28 Z0 (one line) in the text box (MDI screen in Mach 3) and hit the Enter key on your keyboard.
6 Finally, to verify that you set it up correctly, hit the Go to Zero button in Mach 3. Your tool bit should be sitting on the top of your work piece (lower left hand corner).