Putting books into the root of the SD card on the Nook is the default.
However, you can specify a directory to put all books in when Sending books to the device: Preferences, Sending books to device, save template. Use / as a path separator. So if you want to have everything in ebooks then change the template to:
Code:
ebooks/{author_sort}/{title}
Note: This will also put the books into ebooks/... in the main memory too.