I'm pretty sure these are defined by the VMT, which is what the materials menu in the importer makes.

So, for example, if you want glowing bits on your item, you click the 'Self Illumination' checkbox, and then add a Shared Illum Mask. That then uses the alpha channel of whatever texture you loaded for the Illum Mask to determine what parts of the item glow, so full white is glowing and black is not (I believe. I haven't done this myself yet). The colour of the glow is determined by the RGB values you enter in the menu.

Transparency I am less sure of. I think that just goes by the alpha of your primary texture, but you have to make sure you're NOT using Base Map Alpha Phong Mask or Base Alpha for the Cube Map Alpha Mask, because those make the Alpha channel determine Phong and/or Reflection instead of the visibility of the texture itself.

thanks! But the transparency... if it's made the way you say it, it wouldn't be posible to make the hat paintable in just some parts and transparent in some parts... Maybe if you could have 2 alfa channels...

Well, i'll try this and see if i can get to something, and again thanks!

I think you'd have to define different materials to different parts of the model so you can have a VMT1 and VMT2, with one of them paintable and one transparent.