NavMesh and mecanim?

So i recently got a simple project running based off the same technique that the mecanim tutorial used for the character controller, I wrote a simple camera script and i was pretty happy with the advantages of it over the normal character controller so i decided i would base my AI system on that. My testing field was a recreation of peaches castle and my ai was a extracted sonic model for comical purposes (i know its sacrilegious but with sega being third party nowadays i think i can get away with out being smited by the game gods)

I like the mecanim method of controlling a character so I made a empty object and added a navmesh and had the AI always watch it, it looped the running animation until it was a distance of 2 away and played the attack animation. Its not always perfect so i was wondering is their anyway to use the navmesh efficiently with the mecanim system?