There really isn't much to Batch Compiler.
You'll want to go to
then setup your stage paths to your compiling .exe's under
Options->Setup->Stage Paths where you link it to your CSG,BSP,VIS, and RAD programs.
Then set your Output variable in the same window under the "Variables" tab.
Then under the CSG tab, on the top right, you'll want to check a box for "WAD File" and link it to the wad file(s) you used for the map.
I would also check the box on the bottom left titled "WAD Auto Detect" so the bsp file only includes the textures that are used.
Batch Compiler has plenty of options, but they are well documented.
Last thing you want to do is make sure at least CSG, BSP, VIS, and RAD are checked on the very right under "Stages" as this is what programs will execute.
Now you just load up your map's .map file next to "Run", and hit Run.
If you need more help just let me know!
Don't forget to save your preset so you don't have to continually set it up every time you run it!
- Here are some images of my presets in case you have any questions.:
Stage path presets
Output variable presets
Batch Presets for cleaning up after compiling.