I use Taskpaper exclusively as an outliner, most recently to outline a fiction book. I have three TP files:
- the outline of the book
- discarded parts of the outline
- notes
I use Ulysses to write the actual book. By default it wants to do everything on iCloud, but it’s pretty easy to configure it so you can with Markdown files in a folders (one per project). You can nest folders to further organize your project. You’re always editing individual documents in Ulysses but in the sidebar you can limit your view per folder.
My structure is like this:
- Root folder (includes the TaskPaper files, and some misc Markdown files)
- Scenes (the whole manuscript)
- Part 1
- Part 2
- etc.
Each Markdown file is a scene (or set of closely inter-related scenes) ranging from 700-2500 words. I haven’t decided how I’ll break them by chapter, yet 
At any moment I can view all the scenes, or just those in a specific part. In Ulysses you can combine files either permanently (merge), visually (glue) or during export. So what I’ll do, eventually, is work chapter sections in my existing text.
I like Taskpaper’s focus but I find that Ulysses ability to work on a single file/scene, coupled with its flexible sidebar, is sufficient for my purposes. I also discovered that I like having the actual manuscript be separate from the outline. I write the former following the later, but sometimes I diverge, and it’s useful not to have to worry about the mechanics of that. I just write the new scene and then go back later to work it in the outline.
Because both I use plain text with both Taskpaper and Ulysses, at its heart this project is just a pile of text files. So I can use Sublime Text, my favorite text editor, to manage everything and make cross-tool edits. For example, if I decide to change a place name from XYZ to ZYX, I can just do a (careful) search-and-replace in the project folder.
Hope this helps.