I want to modify Koji head a little in he has a damaged eye and have the lid shut, with a scar running down as face as per rough example.

Is this done in Poser, UV mapper or what.
Do I need to remove the eye from obj or just keep lid closed.
And how do I extract the changes I made from the original?

WIP
http://www.frankly3d.com/wip/wip_koji.jpg

it's done as a bump/displacement map on a template of the head texture, which one can generate in uvmapper. I would just keep the lid closed. don't understand third question, as the new bump map is separate from your original texture map.

(Part 3)

I was hoping along with the scar , a physical depression could be put in the skull.

there is no skull - just the surface polygons you see, which represent the face skin. the displacement map causes the rendering engine to produce a result that will resemble a physical depression.