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.