Add the destination directory to the start of the template on the first page of the driver configuration (KoboTouch or KoboTouchExtended). The template I use is:
Code:
Elib/{author_sort:sublist(0,1,&)}/{title} - {authors:sublist(0,1,&)}
Elib is the directory all ebooks sent by calibre are stored under. The author-sort and authors are limited to the first entry by the sublist item to keep paths short.