Personally I much prefer the Rap Genius model of highlighting the actual text being commented on and opening it up by clicking on said highlighted text.

I used to build paperless case management systems for attorneys (I sold that company several years ago now)and I think my clients would have loved to have anything close to this, but I still believe the Rap Genius model is highly superior for ease of use/quality of understanding exactly which parts of a document are being talked about.

Just my $.02