Jennifer,
A few thoughts on your questions......
- I don't believe it's possible to provide a definite answer on that, as there are many variables. Whether you get an automatic will likely depend on how many they have in their fleet, how many they have at the location at the time you're renting, etc. Renting at an airport location may cost a bit more but you may be more likely to get an automatic there. Manual transmission cars are by far more prevalent in Europe.
- I'll leave that question to Roberto or one of the others.
As this is your first time renting a car in Europe, there are a few potentially expensive caveats you'll need to be aware of....
It's important to note that for driving in Italy, each driver listed on the rental form must have the compulsory International Driver's Permit, which is used in conjunction with your home D.L. (so you must carry both). These are valid for one year, and easily obtained at any CAA/AAA office (two Passport-sized photos required, which may be provided by the issuing office).
You may also want to have a look at some of the posts on the forum concerning the dreaded Zona Traffico Limitato (limited traffic) areas that are becoming increasingly prevalent in many Italian towns & cities (especially Florence!). Some of these are enforced by automated cameras and some by local police. Each pass through one of the automated Cameras will result in a €100+ ticket and visitors often don’t know of these violations until several months after they’ve returned home. In addition to the actual fines, renters will also be charged by the rental agencies for providing information to the authorities. You may find this website helpful - http://www.slowtrav.com/italy/driving/traffic_cameras_speeding.htm
There’s also the possibility of fines for driving in bus lanes, parking tickets, tolls and speed cameras including the devious Traffic Tutor system which not only monitors instantaneous speeds but also average between two points. Violate either or both parameter and expensive tickets will follow! Be sure to budget for the high fuel costs and note that some automated fuel pumps may only accept Chip & PIN credit cards.
A GPS along with a good Map is also prudent. Be sure to give some thought to the question of CDW and theft insurance. In Italy, buying CDW from the rental firm is usually compulsory, so coverage provided by credit cards will not apply. Check the Car Rental guide at http://www.gemut.com/ for more information. Their free "Car Rental" PDF Guide can be downloaded. You may also want to check the “Travel & Transportation” pages at https://travel.state.gov/content/passports/en/country/italy.html for other tips. There’s also this website - https://it.usembassy.gov/u-s-citizen-services/local-resources-of-u-s-citizens/transportation-driving/?_ga=1.21563186.86862954.1474991758
Parking in Siena can be difficult to find at times, so you may want to choose a hotel that provides free parking.
In addition to the issues with driving in Italy, there are also some potentially expensive caveats to be aware of when using trains and other public transit in Italy. If you need more information on those, post another note here.