The easiest solution is to rent the car at the airport in Atlanta (lots of rental car options there) and drop it off in Savannah. Expect to pay a fairly hefty penalty for a one-way rental, but it may not be too onerous. But any way you look at it, an airport rental is going to be both easier and cheaper in all likelihood.

I should have added if you want to rent somewhere in Atlanta and aren't willing to go to the airport, then look at Enterprise. That company specializes in non-airport rentals and usually has decent rates.

The best places to start are Kayak.com and Hotwire. Both permit you to specify where you want to pick up the car (either at the airport, or downtown, or in the suburbs, or any combination and permutation you might want) and where you want to drop it off. Note that, with Hotwire, you won't know which rental agency you'll get till after you put down your money -- but, in renting vehicles, I've found that a car is a car, no matter from whom you rent it.

Note also that there are some rental place in the Buckhead area that are just a few blocks from the MARTA stop. Last fall, when I did something similar to what you're doing, I found that a little flexibility saved a lot of money.