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When I obtained a kobo for my husband, I made the following changes to calibre
1) Using the metadata plugboard to add series information to the beginning of titles sent to the kobo as follows
{series:re(([^\s])[^\s]+(\s|$),\1)}{series_index:0>2s| - | - }{title}
(This was so that he could sort by series order since that isn't an available option on his kobo)
I also created a custom column 'genre' and set the plugin to create bookshelves based on the genre and series columns and to automatically delete empty bookshelves.
Otherwise I use the default settings.
I created a custom column instead of just using tags to set up bookshelves because my husband didn't need or want bookshelves based on my tagging system (I use tablets for ereading).
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