Whatever you can fit into your car, you can take. As far as actually bringing bags onto the train, you're only going to need an overnight bag.
I happen to enjoy the Autotrain. The only negative about taking the train is the possiblility of delays. During our last Autotrain trip, we were delayed a few hours because something (don't know exactly what) fell onto the tracks and it took time to remove it. Other than that, the trip was fine! Any questions, just pm me!