One PDF contains the ability to mark a file or folder as a Chapter Marker. A file or folder marked as a Chapter Marker will be included in the "Table of Contents" or "Bookmarks" section of your PDF viewer.
To mark a file or folder as a Chapter Marker, use the chapter marker button to the left of the file or folder's name. The chapter marker button is only visible when your mouse is hovering over the file or folder, unless the file or folder is a chapter marker or is selected.
Bookmarks are "empty" files that act as extra chapter markers. To add a bookmark, right-click anywhere in the PDF Constructor View and select "New Bookmark".