Can you explain what you are trying to do a bit better?
the Kindle can handle books in subfolders, and calibre can send them to subfolders, in the attached USB storage.
But there is no "Main" folder.
Once on the device, collections have to be managed via the Kindle UI. If what you are talking about is collections, that is. Which you haven't made clear.
Also, calibre will see ALL the books on your device, if you switch to Device View.
The "On Device" column only shows books that are both on the device and in calibre, and calibre will rely on heuristic matching to determine which books match.
In Device View you can right-click and select Match Books to teach calibre which Device books match which Library books.