Alpha channels

Ive been looking through the tutorials and i cant find what the differance is between the transparancy alpha channel, and the team colour alpha channel.

Also while im on the subject, why when i screw around with colour balance and brightness dose the alpha channel stop working, resulting in my terrain overlapping to have large white areas?

I'ts pre-set in the model what parts are team color and which parts are transparancy. BAsicly meaning that if you alphaed the entire skin, some parts would be the team color and some parts would be transparent. If you really want to change it, you'll need to do some model edits.