Scrivener and Ulysses are examples of writing applications that are very different from your usual text editors such as Microsoft Word. They do not stress layout, tables, or other word processor power elements; instead, they focus on text that can be outputted in various ways, depending on your needs.
Scrivener and Ulysses are really something like massive writing apps. They allow you to create projects with multiple sub-documents and, in the case of Scrivener, various file types as research. This is useful if you are creating a book, novel, class, series of lectures, and so on. Everything can be in one place, easily editable, instead of switching between various files and folders.
You can sort of get this effect with folders, but it’s not nearly as fluid or simple. If you use a folder and want to move a section from one chapter to another, for example, you would have to carefully work with 2 documents, switching between them. (Scrivener has a really handy “append” feature for this, by the way.) It’s hard to see the various sections in relation to one another, because Word is oriented around the single document structure. It doesn’t work well with a large document with many sections that require constant navigation.
You could also use Evernote or a similar app that allows for multiple sub-documents, but it’s not a great writing environment for polished material. It doesn’t have pagination and footnotes, for example.
Scrivener and Ulysses are so interesting because they are a genuinely different way of writing, as they consider the scope of the project from the outset, and allow for the creation of these sections of material, such as chapters or sessions.
The raw power of Scrivener and Ulysses to hold lots of sub-documents is part of the challenge to using them. It’s very easy to throw lots of ideas into them, and pretty soon the project is unmanageable. Speaking from experience, this is a terrible temptation and problem. Like a good to-do manager, you should keep the project as lean as possible; just because you can add nearly infinite amounts of data does not mean you should. Be circumspect with your ideas and notes, or be prepared for several days of cleaning up.