Hi, I'm OK with most of the wiring to the MB3 but can't find an example for the index encoder.

I'm using a OMRON E6B2-CWZ6C Rotary Encoder, I need index Z and incremental A or B channel.

Here is the encoder pdf  https://assets.omron.eu/downloads/latest/datasheet/en/q085_e6b2-c_incremental_rotary_encoder_40_mm_datasheet_en.pdf?v=8

Also the MB3 manual, it has every example except for a rotary encoder. I have posted on the cncroom forum but it seems dead.
https://cncroom.com/wp-content/uploads/downloads/MB3-Owner-Manual-E20R2.pdf

I want to run the encoder in Counter clockwise (CCW) mode, do I use A or B?

Any help appreciated

What are you using the encoder for?

In most cases you need A and B to give you the count, the Z channel can be used with the homing but you also need a switch to say you are close to the home position and then use the Z channel to find the exact point.  So you need a motion card that can handle precise homing or 2 stage homing or slow down homing or what ever they call it on there system.