Ask HN: How do you gents make blueprints for your web application idea?

I have to take over the Ruby on Rails code for a startup idea that I agreed to be a part of. It was done by a developer hired for a month from odesk (he didn't do much; lots of arguing and disappointment from my partner; it wasn't my idea to get this guy and this was all before I got on board).

I've yet to truly examine this guy's code, and to be honest I have a fear that I'll come across something I don't understand. I'm trying to get serious about this idea and to take on building it, so I was hoping I could get some expert opinion on how one should map out their website idea's functionality? Any specific diagramming software? Or just tons of pencil and paper?

Thank you.