The Bundler component takes care of bundling your scripts at buildtime and extracting the bundle during runtime. More specifically, it turns everything under your Editor WorkingDir into a zip at buildtime. And at runtime, the Bundler will extract the zip into your Player WorkingDir. In most cases, you don't need to worry about the bundling and extraction process as they are automatic.
It's worth noting that it's okay to have multiple ScriptEngines in your scene(s). Just be mindful that during build, every instance of the Bundler component (found in all scenes in your Build Settings) will run the bundling process. So if you do have multiple Bundlers and Working Directories, you may want to have separate sets of assets (i.e. ScriptsBundle.zip, ScriptLib.zip, etc) for each of the Bundler. To do that, you can just duplicate the existing ones and drag the new ones to a different Bundler accordingly.