I have never checked where SRL would eventually store files as I only use it to create collections. I never tinkered with synching and such before.
This may come from older experiences made with mp3-players. Tag all music, add album art, sync it with the player, find out that band A suddenly has album art from Band XYZ...
I finally have my music like I want it to be besides some minor glitches. But it took really long to get there. So I don't bother doing that for my books.