First step, don't carve ;<
Second, the easiest way to make buildings is going to be to make each brush individually, or with the clip tool, or to use textures with windows on them already. Carving will ruin your brushwork so it's advisable to not use it.
The color problem is indeed the 'model' textures. Models are cheap to render in Source because they use a cheap lighting method. (Vertex Lit, as opposed to Lightmapped.) The model textures are defined as VertexLitGeneric in their nfo files (vmts) and they won't be useable on something that's to be lightmapped (ie a brush.)
You can indeed make models for windows in Softimage (which is really crappy imo :p) or another Source-supported modelling program. (3DS max, my personal preference) or Maya, for example. I'd advise against learning modelling in the beginning, though, unless you're really interested in it, though, and save it for later on in your mapping.
If you have any more questions, catch me in IRC or on MSN.