Templates (send to device) can do a lot.
Back when I started, my device only used folders (no bookshelf system)
Chaley helped me out.
To give you an idea (you could just use a Tag as a trigger instead)
Code:
# Calibre Send to Device 11/2013
program:test(field('series'),strcat(
substr(field('series'), 0, 1),template("-series/{series:subitems(0,1)||/}{series:subitems(1,2)||/}{series_index:0>5.2s}-{title}_{authors}")
),template("00noseries/{author_sort[0]}_authors/{authors}/{title}-{authors}_{id}")
)
What this did was separate Series and 00noSeries (top folders)
To keep things neater (no easy way to search )
I then created folders by first letter (for both Series or Authors) to narrow things down for easy location.
Not being familiar with KopReadr. Calibre also has a PLUGBOARD, the can do all sorts of stuff with standard metadata based systems (Does not affect the LIBRARY). eg prepend {series_index}-to Title