In addition to the automated collections, if you're using calibre to manage your books, you can make calibre send the books into specific folders based on the collection structure you want.
if you go to Settings > Sending books to devices, under template you'll see something like the following.
Code:
{title} - {Author} ({id})
You can put a "{#collections}/" at the beginning and calibre will create the collections as folders and then you can put them to collections automatically.. #collections is a custom column in this use-case.
You can go as complicated as you like. I recommend that you use the Template editor. If you multiselect a bunch of books before going into settings and template editor, it will show you real-time what paths you will be ending up on your device using the syntax you designed in the editor.
Code:
{#collections}/{title} - {Author} ({id})
Here's what mine looks like:
Code:
{#collections:contains(^read$,read,)}{#collections:contains(^next-up$,next-up,)}{#collections:contains(^unread$,unread,)}{#collections:contains(^((un)?read)|(next-up)$,,archived)}/{title} - {Author} ({id})