Yes, they normally say 1 bag per person, but I've never seen them be really picky about this.
My normal packing list for on the train consists of:
Pillow with a flat sheet and a light blanket slid inside the pillowcase with the pillow. (use the flat sheet to cover the seat you are sleeping on, much more comfortable than trying to lay against a seat hundreds of people have been sitting in).
A gallon size baggie containing: small bar of soap, wash cloth and hand towel, small toothpaste, toothbrush and deodorant. Using those paper towels is no fun when trying to take a "sponge" bath to clean up in the morning.
A change of top/shirt and a change of underwear. (I can wear the same outside clothes, but NOT the same underwear

)
A CD player and our portable DVD player. Maybe a book or magazine.
With kids, I'd definately take along some of their favorite "diversions".
Any necessary medications.
I pack all the stuff but the pillow/sheet etc in a carry on bag then just carry the pillow, etc.. in a lg plastic bag.
DH also takes along a small cooler containing a couple of sodas and maybe a few cans of beer. There are enough snacks, etc.... available on the train. There have also been times that DH has purchased a pizza at Wolfgang Puck Express before leaving DTD (always our last stop before leaving) and carried that onboard with him - no problem. ( Others looked on enviously

as he enjoyed his cold pizza later in the evening).
They do provide very small pillows (about 10 in X 6 in) which are good to stuff in the space between the 2 adjoining seats, but that is about all they are good for. Also provided is a blanket, which may be useful for a small child, but definately not an adult.
Take along whatever you feel will keep you comfortable.
After many, many trips on the Auto train, this list is pared down as far as I can get it for my/DH's comfort. I have seen people board with only a very small carry on/backpack. It all depends on what you need to keep you comfortable.
Hope you have a great AutoTrain trip.