I have one folder for books I have compiled in Logos.
I have another folder for books I am working on to compile when I am finished. As I have time, I work on these files.
I have another folder for my .docx files that I don't want to compile. i.e Studies, letters, old sermons,
Might depend how many PB's you have.I have a folder of compiled books sorted into subfolders named by Author.
I have a second folder of books to compile someday sorted into subfolders named by Author.
Just because...I also keep a backup of all .lbspbb files. If anything should go wrong, I can rescan them to save losses, recompile time, or move to another computer.
I have one main folder for all my docx files (and associated jpgs), but I have subfolders for books that are more involved than just one file, or which are still in progress or which I hope to get around to someday.