Same as I do for music. I use Calibre and do a lot of manual organization. My tree looks like this:

King, Stephen/

Christine/

    Christine.epub

Dark Tower, The - 01 - Gunslinger, The/

    Dark Tower, The - 01 - Gunslinger, The.epub

Dark Tower, The - 02 - Drawing of the Three, The/

    Dark Tower, The - 02 - Drawing of the Three, The.epub

Needful Things/

    Neefdul Things.epub

Of course, most of my books are fiction so I don’t use genres, but now I’m rethinking that lol.