In Scrivener itself, you could experiment with a combination of keywords, labels, and collections. (I can’t help you with organizing keywords because I’m trying to figure out my own mess (!).)
A Collection is basically a flexible folder or container. You can create a Collection manually or through a saved search; I prefer to create a Collection manually by dragging found documents into a collection, because I usually want to add/remove files manually to that collection.
So, say you know you’re starting with 10 overarching areas, and you’ve begun tagging documents with these keywords. (I’m using ‘tag’ interchangeably with ‘keyword.’)
You go through and tag a bunch of documents/snippets with Keyword1, Keyword2, etc. Then, you can create a collection called Keyword1 (etc.). And another collection that pulls several keywords together. Or tag documents as “To be filed”… Collections aren’t fixed like folders, they corral documents and documents can be in multiple collections. When you select the Collection’s documents in the binder, you can see them in the usual ways: Corkboard, Outline, Scrivenings. (The manual has a lot of info on how to work with Collections.)
Or, create a collection based on a question/topic, and drag documents into it.
The trick with keywords, I think, is to keep them pared and organized (something I have trouble with). Also, it’s really useful to keep a research log/journal. I have a separate folder, “Research Log,” in which I’ll jot quick notes about what I’ve been working on/researching/pondering. These ideas are from Andrew Abbott’s “Digital Paper : a manual for research and writing with library and internet materials.” (It’s geared toward academic writers.)
You could also get adventurous and layer keywords with labels, using a combination of top-level labels and more fine-grained keywords. Keywords can also be nested, but I haven’t played with this much.
I keep my sources in Bookends, and I have separate Scrivener files for my research/writing process and materials (“Notebook”) and for my draft: so, I collect and process material in one file , and I craft and draft in the other. Edit: Actually, on second thought: for a nonfiction research project, a single Scrivener file could work better (I’m writing fiction now)–then you could use split screens, open another document (for reference or drafting, or notes) in Quick Reference and/or the new copyholders, and draft-brainstorm away in your main document with the others available for reference. Lots of options for having your research, notes and draft all available.
And also definitely paper.
Let us know what you decide.