I visited a website yesterday (on the iPad of course) and noticed they had their monthly newsletter available as a PDF download. Not knowing how it would work, I clicked the link and found the PDF downloaded and installed itself on the bookshelf in a separate PDFs section. Now I'm wondering how to get PDFs there that come from other sources - like dropbox. I need to experiment with that.
You can make Dropbox "Open In" a PDF file in iBooks.
While in the Dropbox app (on your iPad), open a PDF file. In the upper right hand side, you'll see an arrow. Press on it and you'll get an "Open In..." dialog box; iBooks should be one of the options you can select. Press on iBooks and the app will open with your PDF loaded (showing).
You'll then see, if you close the PDF file, that it shows up in iBooks under PDF's (in "Collections"). As far as I know, it'll stay there until you delete/remove it.
Hope this helps.
Marilyn
P.S. To keep this somewhat on topic, I've stored textbooks in Dropbox and then opened them with iBooks, Kindle, Stanza and/or Bluefire readers. Awesome thing, that Dropbox! So, you could download any type of ebook and stick it in Dropbox ... the "Open In" function will then allow you to, well, open the ebook in almost any reader you have loaded on the iPad...