Help+Manual automatically adds your project's Baggage files, graphic files and any other files and folders you include in your project folder to the central TFS project on the server. To be managed automatically by Help+Manual, the only requirement is that all these folders must be inside your Help+Manual project folder.
All the files you add to the Baggage Files section are included in the repository automatically. Similarly, if you add folders inside the project folder of your local project working copy, Help+Manual will automatically add them and their contents to the central TFS copy when you synchronize the project from within Help+Manual. You don't need to do anything to include these files in your TFS version control system.
By the same token, you cannot include anything outside the project folder in your TFS project. For anything to be managed in the central TFS project, it must be added to the project folder of your working copy.