The car is the best option for visiting the Tuscan or Umbrian hill top towns. Buses are infrequent and rail is often not even an option at all.
However ancient towns and cities were not built for cars, the streets are very narrow, parking is not available inside and most municipalities have posed traffic restrictions (called Zona Traffico Limitato or ZTL). They basically mean that you need to park in a parking lot outside the historical centers and walk inside the city towns from there. In most cases it's no more than a few hundred meters (yards) walk in small towns. In cities like Florence or Siena, it might be a bit more as they are bigger.
For these reasons you have to choose your accommodations carefully. Hotels or apartments in Siena or other towns may be inside the ZTL (i.e. inside the ancient core of a town), and if you choose one of them, you may not be able to drive to it with your car. You would then need to park away from it and then walk. But there are also plenty of options still in town, but outside the ZTL with plenty of parking in the premises of the hotel, or even outside of town altogether in the countryside (if you prefer that kind of accommodations). There are plenty of villas or old farmhouses (called agriturismo) out of town that have been converted into hotels.
That part of the search requires a bit of homework on your part. You need to search the hotel in various search engines (booking.com, venere.com, tripadvisor.com), then go to the hotel website and see what it looks like, and if it has parking. Also google maps will give you an idea of where it is located. If inside the core of town or at the edges or out in the countryside. Also you can see Google Maps in a certain area. Then enter in the search box: Hotels. It will show plenty of red dots where accommodations are.
For example this hotel here is in Monteriggioni, seconds from the freeway entrance and just minutes from Siena. It's inside the walled village but it looks like it might have parking. There are plenty of options like this, even at a much lower price. You just need to search and inquire if necessary.
http://hotelmonteriggioni.net/
The hotels here are in Siena. In town but outside the old city center, so certainly with car parking available:
http://www.gardenhotel.it/en/
http://www.villaliberty.it/en/
If you choose "out of town" accommodations, in villas or farmhouses, you will never have trouble parking. In town, it depends. You need to do some more homework.
In terms of restaurant options, they are everywhere, in town and out in the countryside. Obviously bigger towns like Siena will have more, but even the smallest villages will have restaurants. Italy lives on tourism. You won't starve, not even in the middle of the boondocks. Some of the best restaurants are in the middle of nowhere. You just need to ask the locals. I remember restaurants where you have to drive a mile on a dirt road driveway just to see where it is. Once you get there, when you lost all hope and you think you are totally lost, there is a hidden restaurant in a farmhouse with a parking lot with plenty of cars and buses full of Japanese tourists.