Just bookmark the current page when you're finished reading or if you want to switch to another book. Double tap the upper right corner (instead of options>notes>bookmark) and you have a bookmark. Once you switched to a different bookmark in another book, double tap the bookmarked page to remove the bookmark and set a new bookmark wherever you finish reading or whenever you want to switch books again.
This way, the notes list is kept short as you have (if you haven't forgotten to "unbookmark" the starting page) only one bookmark per book (which would be tha last page read in that book).
If you forget to unbookmark a couple of times per book, press options while you have a book open, go to notes (or so), press options again and delete all bookmarks. After that press the return button in the left upper corner and set a new bookmark.
I hope this doesn't sound confusing and maybe it helps.
Double tapping sometimes doesn't set the bookmark immediately and instead (depending on your timing) can bring up the dictionary on a random word. But you'll get the hang to it.
