Make sure your financing is ready to go before you start looking. Make sure you know how much you are qualified for and that you have proof of that financing that you can either email or fax. No matter where you go to purchase a car, they are going to want to make sure you can pay. If you do not yet have financing set up, Eloan is a good bet. They are easy to work with and work with online vendors all the time (see Resources below).
Do your research and know what kind of car you want to get before to start. While you can still look around as you would on a traditional car lot, you can't actually see the car, and test drives are out of the question. Plus, there is such a variety of cars to choose from that you will start getting confused after a few minutes. Know what you want or at least narrow your choices down to a handful before you start seriously looking.
Start looking at various sites for your car. A few such sites are listed below in the Resources section. Ebay is also a good place to look, and you can usually get great deals if you are willing to go through the bidding process (see Resources below).
Ask any and all questions that come to mind about the car. Have the seller send you extra photos. Check out and make sure the seller has a good reputation. You can do this through the Online Better Business Bureau, Consumer Reports or the Seller's Feedback on eBay (see Resources below). Make sure the car comes with a warranty so you can make sure you are happy with your purchase and make sure you are aware of the down payment amount before you agree to purchase.
After you agree to purchase the car, send the seller the down payment and proof of financing. The seller will usually want this within 24 hours. Make arrangements to pick up your car or have it delivered. Most sellers are going to want to complete the transaction within 2 weeks of your purchase agreement.