Latest firmware compatible with CNC milling?

Hello,

I was wondering if the latest firmware will allow the Z-axis to move into the negative numbers like the version witch is linked in the CNC milling manual.
I am asking this because the link that is given in the manual is no longer valid. And i am planning on getting the Z-axis upgrade that will require another (newer) firmware.
If i can find and modify the CNC firmware to play nice with the Z-axis upgrade i will still be a happy man. I would still like to be able to use the 3D-printing capabilities offcourse, prefferably without changing firmware all the time.
I am planning to do away with the chemicals for PCB making and would love to be able to still make my own housings without reprogramming all the time.

Any input is greatly appreciated,

Freddy