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Categorizing the pdf assets from within iPad or iPod is possible now. But I think it is more elegant if I can make the categorization from within iTunes in advance.
Is it possible to arrange or categorize the imported pdf assets from within iTunes first and then sync the devices (iPod,iPad) with iTunes?
You might want to look at Calibre. Famously one of the ugliest Mac apps ever created (although it's much nicer looking now), Calibre is an e-book manager. You can use it to process your books, categorize them, tidy up the metadata etc. and then hit "send to device" to copy the books into iTunes.
I originally used it because my ePub collection for my Sony Reader was in it, and so it was the easiest way to get that to my iPad, but I've stuck with it because it has lots more features than iTunes.
Within iTunes-Books, you can view all the ePub books and PDFs you have available to sync to your iPhone or iPad. The PDFs will have a spiral bound edge and the ePubs have either a brown generic cover, the cover art included in the download or the cover art you added via "Get Info"-"Artwork". If you rename the PDF with a number (01-10...) before the title, it will automatically sort via name and put the 01s together Alphabetically and so on down the number line. This is not as nice as setting up a "compilation" like you can do with audio books or multi-CD albums but it should sort your PDFs for you.
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.
