I'd recommend using single folders deep in your SD card.
Folders inside of folders inside of folders 3 levels deep has been known to cause problems. Personally I just make a folder of an authors name or a genre and drop the books in that folder. You can also use a ! in front of a name to keep certain folders in the top 8.
!readfirst
!Baenbooks
!Haggard, HR
!Tolkien
Etc.
Once you start getting a couple of thousand books on an SD card every little trick helps.
I would avoid large numbers of unsorted books in the root. A few is fine but get enough there and you'll start seeing page turns take longer, etc.
Manybooks.net for the PG books, easier to navigate IMO. Plus a choice of format's.
Say I am browsing and I come across something by H Rider Haggard that looks interesting. I can click on the authors name and get a list of all the books they have available for that author. You can then go down the list and get the books in the format you prefer. Many like Epub, or mobi, I have turned into a .rtf fan. But suit yourself.
Or download the same book in 4 formats and you decide what looks best.
Last of all, welcome to the Club! Hope you enjoy yours as much as I've loved mine.