As far as booking, it's all the same, but you might want to look into joining one of the frequent renter clubs. One way to ensure the lowest rate in (almost) any city is to rent out of the airport. They have the most cars, cut the best deals, and are almost always corporate, so you don't have to worry about certain special rate deals not applying or whatever. Make sure that, no matter what, you do a thorough inspection of the car before you leave the lot, and all damage is reported. I've never been screwed this way, but I know plenty of people who have.
Edit: Do not purchase their insurance plans (9 out of 10 credit cards have built in coverage), and do not go for their gas refill plan, they will charge you up to 3x the local price.