You can only index whole folders, skipping some subfolders (at any depth) you manually add to the relevant pane.
You can't skip from indexing files or folders based on their tag, but you can use tags at search time (this applies to files tagged individually; you can't tag a folder to mark all the files its contains):
- use the "by Tag" categorizer in the left pane to filter the found files
- or add a [tags] criterion
- or add a [then apply advanced filter] [tags] criterion