Thanks, but no thanks. No need for slaves. I'd just automate their work away anyhow.
I understand your request, deal with extra files other than the movie, but that's actually a bit tricky once you look at it closer because FileBot doesn't assume anything about your existing folder structure.
There's various ways to tackle this problem though. Are you using the GUI? The command-line tools? Simple -rename calls or the amc script?
Presumably, you're using the GUI. In this case you can select the folders and link-drop them into FileBot. In this case, the folders will be added to the "Original Files" list as single "Folder" item and processed as if that folder was a single unit. Since a folder is processed as single unit, any files or folders inside remain unmodified. If you want to also rename the movie files, and not just the movie folders, then you need to do that in a second step.