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If you don't let iTunes manage your music then music, movies, and books are left where you copied from them and only imported into iTunes as a link as it were. This way you can have your own back up strategy and not duplicate files
This can be a problem, as it was for me since I have "original" epubs I made that I liked to keep untouched - most epub apps make changes to the files as they use them. I copied my epubs into iTunes and didn't think of this and now I've got a new file "iTunesMetadata.plist" added to each one.
I've only got the Winnie the Pooh ebook from iBooks and it's stored exactly like Trubu said; iTunes Media / Books / A.A. Milne which makes more sense than putting books in your music folder.
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