I started using the Balsamiq breadboard prototype tool for quick prototypes, which is good for the early stages of the layout, but it might be too simple for what you want.
http://balsamiq.com/
There is a web demo that you can try, my favorite feature is that it does not look like a finished product, so it holds things that look like βprototypesβ accordingly. I tried sketchflow after watching the incredible demo video, but it was much more unsuccessful and unreliable when I tried it for myself, and I spent more time fighting it than coding, so I just dropped it and returned to the Balsamiq tool.
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