If I have a third party shell module installed, let's just say homebrew, and I have a run shell script block in Automator. If I now type a command that would just work fine in Terminal, what do I do in Automator? Let's say for example I have brew install brightness, it won't run in Automator
You have to specify the entire path to the executable, in this case /usr/local/bin/brew/. Many if not all third-party shell utilities are in the directory /usr/local/bin/.