The way I have my library laid out is similar to the topical grouping on arXiv. So I have a “Computer Science” subdir, and this dir has maybe 40 sub-dirs, organized by topic, and I store each paper in the appropriate location. I also have subdirs for non-arxiv topics that I like to separate out as well (e.g., cooking books, novels, etc.).
This is useful because I have this whole thing stored online, and if I’m on mobile, I may be accessing the files that way (that is, directly, rather than through JabRef, so grouping them by topic outside of the bibtex system is useful when locating things).
I also have JabRef groups, but I use manual groups to organize things by topic or a paper I’m working on or something like that, which may cross sub-dir boundaries.
So, when I download a file, I liked the previous method where JabRef would pop up the dialog box and confirm the file name, because I could then quickly input the path prefix where I want it stored. Now, I have to download it, navigate through my file system, move the file, then go back and change the file entry to point to the new location, which is a bit of a pain.
Perhaps this is not a great system that I have, and I’m open to suggestions, but that is how I do it.
Hope that makes sense.