[ps67]

Kobo library is not based on a file manager but it relies on a Data Base by which You can order Your books for Author, for title, for series (and series information must come from Kobo or calibre) and for collection (You can set Your collection directly on the device or using calibre). And, as You can see, each of that order selection can be ordered in some ways as by recent reading, by name ecc.

Personally I prefer that organization of my books, I don't need to know the real structure of files in my Kobo, but of course other persons can have their own preferences.

However if You really like a file manager structure You could install KOReader that has a file manager by which You can search Your books. It is a very good program and works well on kobos.

Another thing You could do is to set calibre to send Your books to kobo in the way You like, respecting the file manager structure that You desire (I don't do it, but I know that it is possible).