One should be able to sort the bookmarks in the navigator pane by order of the location of the target within the document. This is not currently possible. I would expect such functionality to be accessible from the right-click context menu on the bookmark branch of the navigator tree, although maybe there are other ideas.
The Navigator sorts by occurrence in the document, the first item comes first. I see no need to change this, on the contrary it would be very much confusing.
(In reply to Heiko Tietze from comment #1) > The Navigator sorts by occurrence in the document, the first item comes > first. I guess you're right. I was confused because the focus in the navigator moves out of the bookmarks area when you click a bookmark. So this is actually WORKSFORME.