You need to configure your Kobo driver (KoboTouch or KoboTouchExtended whichever it is you use). The option you want is the 'Save template' box at the bottom of the first tabbed page (File Formats).
ETA: In case it helps my Save template is very simple because I only keep about 200 books on the device. I use
Code:
Books/{author_sort} - {title}