Check out the Audyssey setup guide in this post . It is by far the most comprehensive guide I have come across and gives some great pointers for running Audyssey. Some of the most important things are to make the environment as quiet as possible while running the Audyssey process and to follow the microphone placement suggestions (use a camera tripod if you have one). I would remove any obstructions like the coffee table between your speakers and the Audyssey mic.
That thread is also a great place if you have any questions