For these tasks you may give the standalone-app noteworks a try:
http://themediahost.de/noteworks
regards
slnread
---------------------[*] I have received many emails asking whether the plugin supports EPUB books, exporting typed notes, or exporting highlighted pieces of text. This is
not the case at the moment: only
handwritten notes in
PDF books/documents can be exported using this plugin. See
this post for more details. Sorry!