I highly disagree with subdirectories such as author based subdirectories because eventually you'll end up with a lot of empty subdirectories. I don't mind book or elib as a directory to place all the books. I have my template when sending to my Kobo as...
Code:
books/{{author} - {series}{series_index:0>2.1f| | - } {Title}
That create one subdirectory that will always have books in it. I will not end up with multiple empty subdirectories. Now if say Kobo Utilizes has the ability to search a directory tree and remove empty subdirectories, that would be different.But it doesn't so I don't want empty subdirectories.