Can you upload pdf's on your ipad instead of buying documents from iBook?
Find the App Store icon on the iPad/iPhone. Write PDF in the search box. You'll find dozens of apps made specifically for reading PDFs. Some cost as little as 99 cents, some lite versions are free.
You can transfer your own PDFs to these apps via email, iTunes, wifi, download them from the Internet, Google Docs, Drop Box... Read the features in the app store before you select the app you want to buy. And read the comments, not all PDF viewers are equal. A popular one is Good Reader, which works well, but I also bought a PDF-specific viewer called Pro something or other and it's awful.
You can annotate PDFs with iAnnotate and PaperPad.