When you view the PDF from a web page or an email you can tap on the PDF. Briefly, at the top right side of the PDF you will see a couple buttons to select. One will be something like Open In iBooks (it depends upon your default) and a second one to choose a different program. In your ace I would touch the one that says "Open in. . .". When you touch that option you should get iAnnnotate.
Since I don't have iAnnotate I am not positive this is going to work. I really hope it does. Let me know, OK?
Sent from my iPad using iPF - Peace