Many new users of WWMT find themselves confused when it comes to the setup of WWMT. This is primarily because there are some specific paths you must set correctly for the automation of WWMT to work.
The Wall Worm Material Library Generator originally created DirectX Materials for all materials. But updates to the VMF Exporter changed the way materials are interpretted. Whenever possible, you should not use DirectX Materials.
Information on creating substance-driven material libraries and generating tri-planar projection textures without need for UV mapping.
Information on outputting the desired alpha settings for your materials.