Team glow is just alpha'ed out parts of the skin. So you need a texturing tool that can see alpha layers and use texture types with them (tga), ect. Gimp is free tool and used by many here.
You can see which parts of a model that will be team colored, and which parts that just become transparent ingame, in Magos war3model editor by going to "Materials" and see if there is a texture called "Replaceable Texture" behind it (above it on the list), if it does, it will be team colored. You can see what material is used for what part of the model by holding down "ctrl" and clicking on the part of the model you want to check.
Hope that made sense.