You can as long as the PDF isn't encrypted. Your success, however, may be a bit spotty. Many pdf's have page headings and these headings will appear in the final text. Furthermore, they won't show at the top of the 'page' on your reader since the page lengths differ.
The main reason I own an iPad is because of pdf's. I highly recommend iAnnotate for pdfs and the iPad. I don't know how it works on the iPhone, but I would check it out if I were you.
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