With WC3 Viewer, open up the custom spell model and check its paths. Skin the main skin or the skins that mostly likely will change the model. Convert the skin to a 32bits .tga and skin it.
Or, if you want to skin a existing spell model, extract the spell effect model by opening up war3.mpq or war3x.mpq located in your Warcraft III folder and browse the mpq to find the model. Once its up, check its used paths and extract those skins and skin them, same thing, save it as a 32bits .tga.