I'm a first time car buyer. What is the first thing I should know when negotiating price with the salesman?

I'm interested in purchasing a 2012 Honda Civic EX-L. I went to the dealership to talk to the salesman, and when we sat down to discuss the price, there were tons of extra fees on top of the MSRP: dealer add-ons, destination fees, a charge for the dealership's cost of marketing and advertising, vehicle theft registration, etc. By the end of it, their starting price was way above what the MSRP. As a first time car buyer, this process is a little intimidating. Where do I begin negotiating, and how do I avoid getting a raw deal?