I really like the bookmark pane giving a quick access to my most important entry points. On the same hand I use the document pane to navigate freely to my documents.
My problem is, that I need to switch between these panes back and forth several times. I would like to have a quicker access, less clicks and a better overview.
Perhaps to have the document and bookmark pane in a single tab would help pretty much!
Ok there are also some other panes existing (tags) or comming (note, comment, …).
What about having a split to the left pane. You could duplicate the pane to top and bottom. For each you could chose, which pane (tag, document, bookmark) to show. So you can freely choose.
Perhaps a three column layout (having one additional pane column on the right) would make more flexibility.