<Show name>/Season <Season Num>/Episode <Episode Num>.<ext>
Also be aware: "The Borgias" <-> "Borgias, The"
Patterns that match against the full path is planned, http://dbr.lighthouseapp.com/projects/36049/tickets/9-episode-patterns-that-match-against-path
Handling of "Blah, The" type series names is something thetvdb's API should probably handle, rather than client code, although it would be pretty easy to add if you think it's worthwhile?
I came to check for same, (check path for show name) look forward to this update.