Getting to the hill towns from Florence

Here's a list of all the Tuscan stations. Sometime the station named may serve more than one town.
http://www.rfi.it/cms/v/index.jsp?vgnextoid=96b9822169639210VgnVCM1000004016f90aRCRD

You may do better with buses than with trains. The main bus station is next to the train station. Buses tend to drop you closer to the center of town, trains may have stations several kilometers away (although local bus transportation is usually available).

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The answer will depend to some extent on which hill towns you want to see. Some have good rail access and many are easily reachable by Bus. Which towns are you interested in seeing (with only a "day or two", you won't be able to see many).

One very easy possibility would be Siena as it's easily reachable from Florence by Bus or train (Bus is the better method as you'll be dropped at Piazza Gramsci right in the main part of town, rather than the rail station which is at the bottom of the hill). You could spend one day visiting the sights of Siena on one day and take a day trip to another nearby town on the second day.

I'm assuming you'll be returning home at the end of your hill town visits? Which airport are you using for the return flight?

When you receive your Rick Steves' Italy guidebook to go with the tour, each town chapter will describe whether transport is better by train or bus or car and this is also summarized on the map on p. 615 or the 2015 edition. To see whether train serves a particular town, try www.trenitalia.com or How to Look Up Train Schedules and Routes Online. Since schedules are changing Dec. 14 and not all published past that date, use earlier dates if you try any online research this month.

I will be flying into and out of Rome.

Tuscany is an area best seen by rental car. There are some cities on train lines, but many cities like San Gimignano and Volterra cannot be reached by train.

I picked up a car in Florence city city and returned it in Orvieto across from the train station. The train ride into Rome was just over an hour from Orvieto, and I didn't have to deal with navigating through the city to return the car.