The "Z axis MPG mode" described in that tech bulletin is something completely different (for controlling depth of plasma or water jet on the fly, using a 3-axis mill control).
If you have two encoder-equipped handwheels, then you just need to connect them to available encoder inputs on your CPU board. You should have five encoder inputs, so you have room for both your servo axes; your spindle encoder; and two handwheels.
The handwheel encoders do need to be 5V differential line driver units. Install DB9M connectors per the diagram on your schematic. If the handwheel encoders do not have index pulse channels, then tie the Z and Z/ inputs (pins 6 and 3) to 5V and COM respectively (pins 9 and 2).
See Machine Parameter 128 in your manual for software configuration instructions.