PDF files in iBooks can not be annotated. Bookmarking a page is pretty much all you can do.
There are quite a few PDF reader/annotation apps available for the iPad that will probably suite you better in this regard. I like PDF Expert for this kind of thing. There are many other PDF apps devoted/specialized for different types of users.
If you are more specific about how/why you want to read and use PDFs' someone is bound to know the ideal app.