You need to save the .wad file to your hard drive.
Then add it to your textures in Hammer's options.
Then use them in your map.
In your batch file, add something like this to your HLCSG line:
hlcsg -wadinclude my_new_textures.wad
This will compile textures from my_new_textures.wad into your BSP so people who DL your map will automatically have the textures too.