If you want an easy means of managing books and series, don't load things manually, but make use of calbre. Create a plugboard that massages the title of books to include the series name (or a short version there of) and the index number of the book.
For instance, I have the following plugboard:
Code:
format: ePub
Device: Kobo
Template: {series:re(([^\s])[^\s]+(\s|$),\1)}{series_index:0>2s| - | - }{title}
Destination field: title
Calibre ensures that books end up in a folder based on the author's name, and the, if the book has any series info present, adds (in my example) an abbreviated version of the series name, followed by the book number in the series, and finally the title.
For instance:
THGttG - 01 - The Hitchhiker's Guide to the Galaxy
THGttG - 02 - The Restaurant at the End of the Universe
and for a normal book
How I Killed Pluto and Why It Had It Coming.