I've never used a G540, so don't want to give the wrong info, but you may be able to just wire the plate to Input #1, if the spindle is tied to ground.
The Auto Tool Zero button in the 1024.set screen does not have any code to auto zero, so it won't do anything without adding code to the button. To add the script to the button, go to Operator >Edit Button Script, and click the Auto Zero button. Then paste your auto zero code in the editor and save.
To use the probe input, in Mach3, go to Ports and Pins, Input pins, and assign the proper pin # to the "Probe" Input.
With the 2010 screenset, if the input pin is working, you should be all set.