Staying in Tuscany

While in Tuscany, we used San Gimingnano as our base for visiting the hilltowns. We stayed in wonderful b&b right outiside of San Gim called Il Vicario (you can check our their reviews on Trip Advisor.) Great b&b, reasonably priced and wonderful hosts. We did not rent a car for our stay in Florence. However, for our trip to San Gim, we did have a rental that we picked up at the airport. We did not want to deal with all the restricted zones in FLorence. Might not be convenient for you as you are coming by train.

Jodi, Tuscany is a big area so there is no place where you can base and easily see it all.
If you like southern Tuscany you can rent a car in Chiusi. This will give you ideas on what you can see http://www.slowtrav.com/italy/tuscany/hs_planning.htm

We left Rome by train and went to Orvieto. We picked up our rental car there. We actually stashed our bags in the car and left it at the rental office, then took to bus up to town. We spent half a day there, then drove to our agriturismo. We stayed at Agriturismo Marciano, located in Siena, but outside the walls. It is actually a winery. It was fabulous. The location, scenery, lodging, etc. was exactly like I pictured an agriturismo to be. And the optional dinners they serve are to die for! Multiple courses of fresh, home-cooked food, accompanied by a different wine for each course. The wines are from their winery. It was the best food we had during our 3 weeks in Italy. They don't offer the dinners every day, but we ate there 2 nights out of our 4. They also serve a delicious breakfast every day, which is included in the very reasonable price. Check out the reviews on Trip Advisor. We found it to be very well located to do day trips to hill town. We returned the car to the airport in Florence.