I rip mine to iso's. I also use xbmc, so I have some experience doing what you want.
I recently ripped a season of 24.
On each dvd there were 4 episodes. I use dvd shrink and I save each episode by itself.
(to do this select 'open disc' in dvd shrink. When it is done analyzing the disc it will show each episode on the right side. Drag one episode to the left side and choose 'backup' and save it to whatever location on your hard drive you want. Do this for each episode seperately)
Now, the way I set it up for xbmc is as follows.
I have a folder called TvShows.
Inside that folder I have a folder called 24.
Inside that I have a folder called Season 1.
And another called Season 2.
For season one, I have all the episodes for that season. Named as follows:
That means the show is 24, the season 01, and episode 01, and episode 02.
Season 2 episodes would be 24.s02e01, 24.s02e02, etc.
BTW, I use media companion for my movies and tv shows instead of the scraper in xbmc. You should check it out.
Revo Ion...XBMC For Windows...Dharma RC2