Quote from our very own Custom textures tutorial:
Including the Textures
...-wadinclude, but this one only works with Zoner's tools (Version 253). Instead of putting all of the textures used in the map into the BSP, it only includes the ones from the WAD(s) you specify. In other words, you can tell it to include only the custom textures that you created. To use it put -wadinclude wadname as your CSG parameter, where wadname is the name of the file. You don't need the extension or path (these will be taken from WorldCraft). So your Parameters box should say something like this:
$path$file -wadinclude mytextures
To add more than one wad file to your .bsp, all you need to do is add another -wadinclude command
$path$file -wadinclude mytextures -wadinclude mytextures2> and so on...
Yes, you have to use the -wadinclude prefix for every new wad that you want included.