I see. From my experience of hearing from our users, it's a preference thing -- some feel that the document structure makes navigation easier, whereas some think it adds too many clutter.
If you're the latter type, my best advice is to hide the left pane to reduce visual clutter and try to use file finder to jump between documents and bookmarks. You could also use internal links to point to the shared document, as if it's a sub-bullet. If those still can't reduce the feeling of clutter, I'm out of ideas. Hopefully maybe one of those ideas might help you!