Just wanted to bump this thread with some more current information, since this is the first result of googleing "Atlanta Amtrak Hertz" (and thus how I found these wonderful forums).
It is basically as PRR 60 stated above, with the exception that the Hertz telephone seems to have been removed - also, when reserving at Hertz, the Hertz website lists the address as 1688 Peachtree, which is the address of the station, NOT the address of the JW Marriott, where the rental office and cars are located. Upon my arrival at the station this morning, none of the cab drivers waiting there knew which Hertz in the area was considered the "Atlanta Amtrak" office (and the only address I had was the wrong one) - a quick call to Hertz's 800 number confirmed that the JW Marriott location (also known as the "Buckhead" Hertz, or the Hertz at the Lenox Square Mall) was the right location to go to.
The cab ride was quick (10 minutes) but a bit costly - $16.25 base fare, plus $2.00 per extra passenger (more than one). Since Hertz will knock off up to 20 bucks in cab fare, I'm going to end up having to eat the cab ride from the Hertz to the Train station on the return. Cars must be returned to the Hertz location and not at the station, which is a little bit of a disappointment. But, armed with the right info, this can be a pretty painless evolution.
Also of note, the Hertz doesn't open until 9:00 on Saturday - 19 actually arrived in ATL about 15 minutes early, so even with the confusion at the station, I was at the rental counter at 8:50, and had to wait until about 9:05 for them to get opened up and ready to go.
Finally, the pre-pay gas rate listed on the sign was $3.69, but the clerk said that the "Atlanta Amtrak" location rate was still listed in the computer at $3.05/gallon - needless to say, I prepaid the fuel and will return as near empty as possible, as I thought that fueling at $3 a gallon was going to be a distant memory.
Anyhow, sorry to drag up such an old thread, but hopefully this will help some other traveler as it did me.