Did you find the All About the Autotrain
http://www.disboards.com/showthread.php?t=402667
thread? 26 pages of info and experiences there.
We took the autotrain south in April 2003 and both ways in April 2005. We did not book a room - just tried to get some sleep in our coach seats. Dh does better than I, which is good because he does most of the long drive back to NY.
Our son was almost 4 on the first trip and almost 6 on the second - he absolutely LOVED it. In fact he preferred it to the airplane trip we took last fall. He likes being able to move around and explore the train, and he does find other kids to play with. The Autotrain usually separates the cars by passenger configuration, one car may be mostly families with babies, then one with school-age kids, then one with just adults. The "kid' car has been fine for us, no crying babies at night, no worries about disturbing the all-adult cars. Each car has it's own restrooms, the only time you travel between them is for meals or to the snack car.
September should have less passengers, but in October you might begin to catch the 'snowbird' crowd going South for the winter months. That is why we couldn't get a seat on the trip North one year, so many of the 'birds were heading home again.
Happy planning. If your son is interested in trains at all he will love it.