Is it true that you can't select multiple files in the Project Manager? This is ridiculous. Online Help Authoring tools are supposed to be able to manage what could be at least 10s of files, if not more. So I'm supposed to spend at least 20 minutes deleting / managing files?! Not to mention that apparently you can't format topics to be sub-topics in a TOC? This is a given in Flare.
Why are you needing to select more than one file?
The Topic List pod allows selecting multiple files.
Additionally, you may have as many levels as makes sense to have in the TOC. It might be helpful to explain how you are attempting to do it. Perhaps you just need some training? If so, I might know a guy that could help.
You use the topic list for that purpose.