Other fees include sales tax, interest for any dealer financing, registration, delivery charge (IIRC), and probably something that I'm forgetting. Your best bet would probably be to see what rate the dealer's financing option is offering and compare it to the rate your bank offers.
Your best bet would be to shop around at several dealers first, using sites like autotrader.com or cars.com. That will give you an idea of what the vehicle you want is going for, and you can work from there. Once you've established a baseline for a vehicle - say a 2007-2008 Fusion, SE V6, with 20-35k miles and a few options (using this example, since that's what I've bought), and a general price range, say $12.5-15k - you can contact each dealership via email to explain what you're looking for and what you're willing to pay. Avoid sounding needy ("I need to get a vehicle before Halloween!") or unsure of yourself ("I'm looking at Altimas, but if it starts snowing soon I might look at a Tundra or Explorer instead... that is, unless you guys happen to have a Miata or S2000 on the lot, I always liked those."). See who's willing to work with you, and make trips to the dealerships to check out the vehicle and work on the file details based on that.
Buying used is somewhat of a mixed bag. Normally for a new vehicle, you just have to consider the vehicle you want, the trim level, and any additional options. When you're looking at used, you also have to factor in mileage, wear and tear, and any damage or bad history. Dealers that are overly eager to work with you may know that the vehicle has some kind of hidden problem, while other dealerships may think their original price is God's gift to America.
I'm sure others can give more tips than I have; I've only bought one vehicle from a dealership in my life (all others have been private party). It can be stressful, but it can be somewhat fun too. They're the ones making the sale, they should work around your schedule (provided it isn't ridiculous...).