I have mine organised in 'My Files' as folders grouped alphabetically i.e. 'A-C' , D - F' and so forth. In that folder, I can find all those letters authors folders alphabetically listed by surname and each authors folder contains books grouped by series and number. Initially I renamed each book file as series then number in that series, now I use calibre to do that. If it is a prolific author, I may also have some large series in a sub folder.
I find this easiest for me. I have all this stored on a micro SD card which I remove to a card reader when adding books and use drag and drop. My Nook ST and Color are both stock standard with no rooting etc.
pretty much everything on my readers is side loaded