Team Color OR Invisible?

I have been skinning a few models lately, and I have read the tutorials talking about team colors here. Right now, just as an example, I am playing with the Druid of the Talon.

I didn't want his new look to have the big, long beard, so I alpha'd it out. Perfect, now the geometry just 'disappears,' giving him the effect of a shorter beard.

Okay, now I don't want that cloak of feathers on his back. Following the same procedure, instead of becoming invisible, it now becomes the team color.

What exactly determines where alpha'd out becomes invisible or a team color? Is there a way to force it into one or the other?

Thanks, and I apologize if this is a naive question.

In the Druid of the Talon model, there is team color on his cape. Any spot on the alpha channel that is black (cape area) will show team color. You have to remove the team color from his cape to alpha it out. Or you could just ask a moddeler in the Request forum to remove the whole cape for you.

A model consists of several geosets, meaning a chunk of vertices and faces.Each geoset can only have one type of render, meaning team colour or transparency (or some other). You can modify the MDL file to swap between these, but you can't have both on the same geoset.

I'd rather learn how to do it myself. =)

How do I remove the team color? I have a variety of modelling tools, but my understanding is that I need to modify some code..?

Also, upon messing with his two capes, he looks very, very strange. This only occurs when lighting is on - when it is off, you see the textures just fine instead of seeing strangely smoothed polys. Anyone seen this problem before?

He looks like this:

Bah. Upon experimentation, it seems that the original model is like this, but it is well concealed by the feathers/teamcolor (I tested this on a different machine to make sure it wasn't my video card/settings). What a bummer... looks like I will have to use a different model, unless someone knows how to actually fix the smoothing.