When you customize plugin for the KoboTouch plugin, your save template goes at the bottom of the Fie formats tab. mine is set to
Code:
books/{author} - {series} {series_index:0>2s|| - } {title}
To get to the KoboTouch plugin, go to Preferences > Plugins and search for KoboTouch.
What version of calibre are you using and what OS?