Ciao Marion,
That agriturismo is in southern Tuscany in the area known as the Val d'Orcia so I would concentrate on exploring the area!
Aside from a day trip to Siena (where you can also fit it the castle of Monteriggioni), I would concentrate on going around the Val d'Orcia to Montalcino (and abbey of Sant'Antimo), San Quirico d'Orcia, Pienza and Montepulciano. Do you want to try some outdoor hot springs? The ones at San Filippo are lovely, there are also smaller outdoor pool in Bagno Vignoni - take a look here:
The incredibly beautiful hot springs and the calcium formations found at Bagni San Filippo make this little town a must-visit on your travels through southern Tuscany!
www.discovertuscany.com
You can enjoy the outdoor hot springs below the town or in one of the famous hotel Spa centers in town in Bagno Vignoni.
www.discovertuscany.com
Visit this enchanting abbey near Montalcino.
www.discovertuscany.com
Read our itinerary and guide of Pienza in Tuscany. Pienza monuments, museums and attractions, what to see in Pienza, south of Siena.
www.discovertuscany.com
Visit San Quirico d’Orcia, one of the most beautiful and charming medieval towns of the Orcia Valley located to the south of Siena. Suggestions and tips on what to see in San Quirico, including monuments, gardens, and churches.
www.discovertuscany.com
Also make time to explore the castle at Sarteano:
https://www.discovertuscany.com/tuscany-destinations/sarteano.html
Then while you're in Perugia, I would focus on Perugia and going to Assisi!
As for driving and parking, most towns have the centers closed off to traffic but all you need to do as you arrive in the towns is follow the "P" parking signs that take you to the parking lots. You will never risk going into the wrong part of town if you head to the parking lots.
