here’s one way I use folders - to incorporate all the research I’m considering / reading for an article I’m writing. I always read more articles than I end up citing, so this folder includes more than the bibliography / references. As come across new papers, I think about how they will fit in my article, and put it in that folder.
Also, I format the subfolders in the same order and hierarchy as the flow of my article. So, the folders go something like this:
Argument 1
sub-argument 1a
sub-argument 1b
argument 2
As I’m writing, the papers I need to cite from are right there in the subfolder that matches the section I’m working on.
Once the article is completed, you could export the papers in the folders for a reading list.