Alpha-ing the hard way
I don't know how the real way is done, or how to get rid of team colour, but the way I make certain parts of the skin disappear is:
1. Select the object with the "Freehan Selection" tool
2. Click on "Layers" at the top of the screen, and from there click "New Mask Layer" and then "Hide Selection"
3. Click "Image" and then click "Delete Alpha Channel"*
4. From there, (in the "Layers" section) click "Load/Save Mask" and click "Save Mask to Alpha
Channel"
5. Then, (in the "Image" section) click "Palette" and "Set Palette Transparency"
6. Click "OK" to the window that comes up, and then click "Set the Transparency Value to Palette Entry" and adjust the number until the colour white shows up in the colour window next to it (the number is usually around 250-255)
Then just save the skin and what you selected should be invisable. I know its a long process, and there is probably an easier way, but I thought you might want to know this way, just incase the other ones don't work.
*when you delete the original aplha channel, it gets rid of any other invisable parts (ex. Evil Illidans wings aren't ripped anymore if you delete the original alpha channel, because the rips were made the same way i make invisable parts)