You can add bookmarks to different pages within an ibook and access them via its Contents Bookmarks Notes screen, but that might not be as sophisticated as you are want.
For the ability to have multiple books open, you can leave feedback for Apple here (these are user-to-user forums and Apple don't monitor them) : http://www.apple.com/feedback/ibooks_ios.html
Hey King Penguin
That's a good point and indeed I was looking at something a little bit more sophisticated. Though I definitely should look a bit more into the bookmarks. Bookmarks, I believe, do not provide a complete answer to what I was describing because often you will navigate from one book to the other looking for something and thus there are not yet bookmarks.
I will post it to the Apple feedback as well but I wanted to see whether others think the same in the forum.