I find it very confusing to get a good workflow with it + calibre.

I sync all of my books (and use readarr for organization or occasionally grabbing books from dead authors) via syncthing. Then calibre web won't ingest any new books I copy to the folder, so I have to go to desktop calibre to add them manually, then it will sync the database and calibre-web has a built-in task for scanning any database changes so then the book will show up.

Seems like a clunky method and I would think I am doing it wrong, but I haven't found a way for calibre to scan books already organized in folders in its book directory.