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.