Here's the deal:
What you see when you look at a model is the texture layered in a material over the mesh.
The mesh is the actual faces, polygons and vertices of the model. It has no texture by itself, but is given lighting by the shader (which isn't important right now). The mesh may be broken up into geosets, which are groups of polygons.
The material is applied to the mesh along with one or more textures to give the mesh detailled colour information. The material can have various blending modes to control the way the texture is displayed. The blending modes interact with the alpha channels on the texture to affect it's transparency.
The texture is the image you draw in photoshop/whatever.
How Team Colour works:
Most WC3 models are cut up into various geosets to allow for team colour. The areas of the model intended to have team colour will usually have a different material to the areas that aren't. The material that has team colour will have at least two layers; one for the team colour texture itself (called Replaceable ID 1) and one for the texture with all the details you've drawn. The layer with the details will usually be set to Blend, so that the areas that you've alpha'd out in the texture will allow the team colour layer underneath to come through.
So, long story short:
You cannot add team colour to geosets which don't have the material set up for it without editing the model.