Very dumb question, but I have read multiable answers so...

I am correct is assuming that most people with gantry style mills setup their Z axis as +10 for top, 0 for part top, and negitive numbers for the cut?

most mill type machines are set up with the Z axis working minus into the work

Graham.

I had thought that as well, but after watching the video's it seems your mill's highest Z point should be set to 0 and you mill down from there. and then you would use an offset, bring the bit down to the surface and zero the Z axis (Not the Mill's Z but the offset Z axis). then if you cut -0.2500 into the surface your cut will come out a quarter inch (if your using inches) into the surface.

This is what i got out of the video's, i might be wrong.