I took a quick look in the
iTunes Music Library.xml and couldn't find my books in there (music, movies, TV shows, podcasts and audiobooks are all in there - books and pdfs are missing). The Book category does not seem to affect the Album/Grouping/Genre metadata of the book (from iPhone to iTunes) and the Album/Grouping/Genre metadata does not seem to affect the Book category (from iTunes to iPhone).
If I remember correctly, the iBooks app asked me if I wanted my bookmarks and other data to be stored on my AppleID account and I confirmed. If the categories are stored along with the bookmarks in the cloud then you are in tough luck until Apple decides to add this functionality to iTunes.