A neat thing about Ulysses is that it is very free-form, and as a consequence, it can adapt to different needs. For a novel, I would create a top-level “group” to hold the project itself. Then I create sub-groups to hold characters, plot and synopsis, locations, to-do notes etc. And of course one group to hold the chapters. Now, the hierarchical nature of the file browser allows me to place each chapter in a group of its own, which means that I can add chapter-specific notes in that folder if I like. If I then add a “chapter” keyword to the chapters, I can easily create a filter to show all chapters in succession, and I can even create separate filters for different revisions if I like.