You need the Zener diodes in place to drain off extra voltage to the ground line.
As I understand it the Zener acts like an overflow valve, turning those high volt injector pulses into low voltage pulses that the ATMEGA chip can safely handle.
Either [No10: "Injector"] or [No20: "Injector"] is what you want to tap into.
Ideally you want to use the car ground and not the ground on the ATMEGA board.
Here is a simple page I made, mainly as a reference for myself but I was hoping it would help others.
How to build an MPGuino - EcoModder
I created the image on that page because all the other ones I found where kinda confusing.