Can you call the folder "Season 0" rather than "Season 00" and have no issues? Otherwise I might as well rename "Season 1" to "Season 01" to keep it looking neat.
I've also just found the program TV Rename, helps a lot, in terms of what episodes/seasons your missing. theRenamer is alright too, easier, but doesn't have that function, its basically just a drag and drop re-namer.
On that note, I really like Ember, for movies I just set the following settings and it works fine in XBMC which will pick up the locally scrape data that Ember created.
You must set Poster to Movie.TBN (xbmc format for images), don't set it to .JPG as it won't scrape it from your HDD, silly old tutorials on the net like this
http://www.howtogeek.com/?post_type=post&p=61976 have too many files checked, you only need 1 per box. This took me a while to figure out.
Also, ticking "movie.nfo" lets you keep the scene nfo (that nfo file that came with your dl) in the same folder, and XBMC will scrape the text information from "movie.nfo". If you use <movie.nfo>, you cannot keep the scene nfo in the same folder.
I just want to re-inform people of the two points above as it took me some time to get the answers/info.
http://i.imgur.com/JmS0h.jpg
Also, one thing I've noticed, I've scrapped my TV shows etc, put it into XBMC, if I'm in TV Shows, press C, update library, I'm getting like double episodes like S01 E1 E1 E2 E2 etc, any ideas why? I did make some custom NFO files for comedy etc, but I don't think its that?