Paint the group with the default material in the places you want the color to change. There are probably a few ways to script this, but one is:
@m = Sketchup.active_model.materials.add "My material"
group.material = @m
@m.color="Red"
"Red" could be any color name, and you do need to use the quotes. Or you can use an r,g,b value... [100,100,100], for example, will give a shade of gray. The name of the material, in this case, "My material", is of no real consequence, as SU will stick a number on the end if the name is already being used. You should be able to change the color during the sim with:
@m.color = ...
In ontick, or whatever. You can also do other stuff with the material, like use a texture, or make it transparent... see The API for more info. Good luck!