Remember that once you add a book to Calibre that you should consider where and how it stores the book as irrelevant. While yes, Calibre DOES use files and directories, those to are a portion of it's database.
What many people do is to use a Plugboard within Calibre to automate the book naming on their eBook reader.
For instance, with me, in Calibre
The Hitchhiker's Guide to the Galaxy is the book's name, by
Douglas Adams in series
The Hitchhiker's Guide to the Galaxy and is number
1.00.
My plugboard is set to
Code:
{series:re(([^\s])[^\s]+(\s|$),\1)}{series_index:0>2s| - | - }{title}
This results in the book on the Kobo appearing as
THGttG - 01 - The Hitchhiker's Guide to the Galaxy by
Douglas Adams. The next book appears as
THGttG - 02 - The Restaurant at the End of the Universe.