Let the user know wheter there are some notes outside current view panel

[carriH]

Idicate to the user if there are some notes that are not visible (because they are down in the page and the user has to scroll it down -or up-).

Faster way is adding a message in the page (how much time should this message be visible? Should it be shown permanently and have a close button to allow the user to close it?).

Better way is adding some colored marks into the scroll, letting the user to know on what places of the page an annotation has been inserted.

[vertigo220]

My personal choice would be the second option. Provides more info (actual number and position of notes/annotations), can allow for clicking the markers to jump to them, and it's unobtrusive. If doing the first option, you could always make it user-customizable as to how long it stays, but otherwise I'd say have it go away after ~5 seconds.