Know your cars and all the options packages, plus invoice prices if you can find them (edmunds.com lists most invoices). You can research options by using the "build your car" features on manufacturer's websites. Have a list of all the local dealers and their phone numbers and addresses. Take this information with you, with that list on top of your stack of information so they know you'll be shopping around.
If you are financing, get pre-approved for a dollar amount by your credit union or bank of choice before going, so you have something to compare to the dealer's finance offer. Know how much you want to put down, too. If you're putting down a healthy, amount, you can absolutely skip any "gap insurance" bullshit that they will try to sell you. Also skip the extended warranties, stolen vehicle locators, or any extra crap they try to tack on the car.
As for buying the car itself, I recommend getting all the above in order, then going early on a free day, and explaining that you are looking to buy a car and that you are ready to buy today, but only for the right deal and that you aren't in any particular rush, and you're going to be shopping around. Test drive the car you are interested in, then explain to the dealer that you will seriously consider buying his car, but you are going to be driving X car and Y car, too, and you're also going to be visiting B dealer and C dealer that sell his car make to see what kinds of deals they might be able to throw together. Ask the salesman what the best price he could sell the car for is. He might go check with his manager, he might offer a handshake offer to "beat the other offers," or he might refuse to talk prices without a firm commitment to buy. The salesperson who says he'll beat the other offers is the guy you'll probably want to buy from at the end of the day.
Then leave and repeat at the other dealers and models of car you are interested in. If you've collected a few offers, call the guy who said he'd beat the offers and give him the lowest price you got and the dealer who gave it to you.
People talk about doing this on the internet, but I've personally never found internet salespeople to be responsive to polite requests for price quotes, so it never works out for me.
If you end doing "blind" negotiations on a specific car (i.e. not playing dealers off each other), then start significantly lower than your target "fair price I'd actually pay." The dealer may balk at reducing the price at all to see if you'll give up. Just say you think your offer is reasonable and you need to see the manager reduce his price before you are willing to raise yours. Then give up $100 here or $200 there, not $500 or $1000 at a time. Make them work for it and make them come down at least once for every time you go up. Don't just sit there while they "think" about your offers. Get up and walk around, look at your watch, make calls on your phone, walk around the sales lot. You want to look like you're ready to walk out at any moment. When they hit the price you have in mind, shake hands and buy the car. Sometimes you can cut through the crap by talking to the manager directly, other times they prefer to keep him behind the curtains like the Wizard of Oz. And if they never hit the price you are willing to pay, don't buy the car.
Negotiate price ONLY, not payments, not financing. Worry about financing beforehand with your bank. If the dealer can beat that rate, then take it. If not, plan on a 60-month loan with the lowest rate you can find and buy based on price, not monthly payment size. If they bust out the "4-square" negotiating paper, use their pen to cross out all the boxes except the price box.
Edit: As for the manual, you can explain that you can drive manual but you aren't very smooth yet, and give the salesperson the option of letting you drive a manual, or an auto for the test drive. He'll probably let you drive the manual as long as you have any experience whatsoever.