I thought it would be simple. It turned out to be simple, but not intuitive.
Here’s how you do it: locate a PDF on your computer and drag it onto the iTunes 9.2 application or the iTunes window’s sidebar. The next time you connect your iPad, the PDF shows up under the Books syncing tab.
So, yes, very simple.
By “not intuitive,” however, I mean that I had to fumble around for quite a while before I had success getting a PDF onto my bookshelf. In fact, the successful method was the third method I tried.
First, I thought that any digital book already in my iTunes music library would be available automagically. I mean, why not? iTunes certainly knows that a digital book purchased from the iTunes store is a PDF, right? It actually says that it’s a “PDF document” right in iTunes. Not so. Any digital books in your music library stay right there: iBooks knows them not. [Side note: I even made a playlist in iTunes that contained only digital books, hoping to sync that playlist to the iPad. However, that playlist didn't even appear under the Music syncing tab in iTunes. D'oh!]
I also tried dragging a PDF I dug up in the Finder into the File Sharing area under the Apps syncing tab. No luck. iBooks doesn’t appear there as an app that understands file sharing.
At last, in some desperation, I dragged the PDF onto the iTunes window’s sidebar. Finally, success.
So, if you want PDFs to appear in iBooks, you have to drop the PDFs directly onto iTunes from the Finder (or from Windows Explorer if that’s the way you roll).
As for the digital books in my iTunes library? They don’t appear in the iBooks collection even if I drag them from their location in my computer’s file system onto iTunes! Really. I don’t know why.
Silly? You betcha!
[Update: You can get the digital books from iTunes albums onto the bookshelf if you first remove the books from your iTunes music library: right-click a digital book in your music library and delete it. Let iTunes put it in the Trash. Then drag it out of the Trash to somewhere else on your computer and then drop the file back onto the iTunes window sidebar or the iTunes application. iTunes then adds it to the Books collection. It's like driving from Boston to Cambridge by way of Saskatoon.]
[Another update: There's an easier way to get digital books from the music library onto the bookshelf. Get Info on the book, click Options, and change the Media Type from Music (!) to Book. The book is listed in the Books collection once you do that, and can be synced to the iPad (or iPhone).]