Wendy, Jon and Ellen's suggestions are right-on-the-money. Stay in Sienna and take the bus (not the train!) back and forth. Rick covers this quite well in his book (except he does not tell you exactly where to get to the busses.....we found good info in our Lonely Planet guidebook.)
Our friends recomended the Hotel Chiusarelli, and that is where we stayed. It is a RS recomended hotel. It is just a basic hotel that is close to everything, busses, the walk into the main part of Sienna. Nothing special, but it does the job. They also said that it had a few parking spots. Check out the reviews on tripadvisor.com.
http://www.tripadvisor.com/Hotel_Review-g187902-d231295-Reviews-Hotel_Chiusarelli-Siena_Tuscany.html
Also check out the Hotel Alex, very reasoanbly priced with fantastic reviews.
http://www.tripadvisor.com/Hotel_Review-g187902-d603927-Reviews-Hotel_Alex-Siena_Tuscany.html