I am not sure I have enough information to provide a specific answer to your question, but perhaps this info can get you started...
If I understand correctly, you are going to provide some UI that will enable the user to point to the location of the annotation when viewing the document, then you will modify the PDF on the server, and render it with the annotation at the point selected by the user.
Perhaps one way you can capture mouse input to enable the user to select the location of the annotation is to render an image of the PDF document page and show it on the page, and then capture the mouse location on a click event.
Then, if you have the annotation and the desired location, you could use a PDF library to update the PDF and draw your annotation into the document on the specified page at the specified X,Y coordinates.
We are using a PDF generation library that we are very happy with to render PDF documents on the web server, which we deliver to the browser via our ASP.NET application.
You might want to take a look at this product and see if it can meet your needs:
DynamicPDF from ceTe software: http://dynamicpdf.com/
Hope this helps.