Yes you can use any book you have to make notes but I am one of those people who simply prefers a separate application for that unless the note-taking is relevant to the book in question.
You can simply make a .txt file with some words in (you need some text to "attach" your notes to) and place that on your Kindle.
Or I prefer to use an online app such as simpletext.ws which is something that also syncs with my iPhone:
http://www.kinworm.com/2010/10/handy...ur-kindle.html