I will soon be taking my 9th AutoTrain trip (October). I have a special needs daughter who does not like to fly so for us the train is a great way to travel. We book bedrooms as opposed to coach and have enjoyed each trip. It's important to book as early as possible for the best rates - they start booking at 11 months out. They have family bedrooms that sleep two adults and two kids, but only a few per train, so again, early booking is better.
We leave out of suburban Philadelphia, usually the night before and stay in Lorton, VA at the Comfort Inn (they have a special Autotrain rate, but you need to call to get it). This way I am not all stressed about getting stuck in traffic the day of departure and missing the train.
The train usually gets to Sanford, FL around 9am and waiting for the car to get unloaded can take up to 1.5 hours or so, if your car is one of the last off (which mine usually seems to be, although once it was the third one unloaded) and then about an hour to WDW from there.
It's nice not to worry about luggage as it all stays in the car, except for what you need to bring on the train for overnight and then you also have the advantage of having your car once you get there.
There are no stops, except for one around midnight where they change some staff and will now let smokers get off the train to smoke - they recently banned all smoking on the train.
Check in for the train starts around noon or as soon as the arriving people have all cleared out. It's best to check in early as tickets for the dining cars are distributed first come first served. The meals are usually 5pm, 7pm and 9pm. When we arrive at the station, we just check in and get our tickets and meal tickets, and then leave the property to get lunch somewhere and then get back around 2pm. Last car accepted is at 3pm. Train departs by 4.
For the return trip, we leave WDW by 1pm. The ride back is never as crowded, and they will sometimes reduce the number of meals to two, at 5:30 and 7:30.
