Syncing a folder structure into iTunes for use in iBooks

I have a directory of PDFs for my recipe collection. Each directory is a different cuisine (eg cajun) or meals (breakfast)

Recipies

..Cajun

..breakfast

..Japanese

Etc

When I add the folder through iTunes, it processes the files (shows a dialog saying so) but when its done nothing is shown in itunes. I think it's because the files are located in a directory structure rather than a bunch of files in a single directory.

Suggestions?