Paint whatever you want team colored black on the diffuse texture, and on the alpha channel paint the details of the black area in black and white, taking into account the fact that black = transparent and white = not transparent on the alpha channel. That only works, however, if the model actually supports the area you want team colored for TC. In case it doesn't, you'll end up with a transparent area rather than team colored, and you'd have to modify the model's materials instead.