Here are the requirements, the users needs to be able to view uploaded PDFs in the browser. They need to be able to add notes to the PDF and save the updated PDF to the ser
You did not specify what technology limitations you have. If you can consider a Silverlight solution, and you have client computers that support Silverlight, you can easily do this.
Take a look at how Microsoft Sketchflow works, it permits the user to annotate documents in the web browser and the annotations are persisted back to the server.
Here is a company with a commercial control to annotate PDF (and other formats).
Microsoft does this in their Sketchflow player. Here is a video. Of course you would not be using sketchflow but rather implimenting something similar that meets your needs.
As an added bonus Silverlight 4 supports the clipboard as well as drag and drop so that end users could paste something onto the PDF immage as well as drag any file onto it ehich you would then be able to upload to your server.