Assisi

Once you are in Assisi, you head out of the city center. We drove. It was a beautiful setting and we were so glad we included this part of Assisi.

Get a cab from the train station to your hotel. I GREATLY RECOMMEND Istituto Beata Angelina. It is right across from the Basilica. Ask for a room on the side with a view. www.monasterystays.com

Not sure what you mean by the "monastery/hermitage".
The train station is down the hill from the main part of the town - maybe a half mile away by taxi. Once there the city is pretty compact as far as the notable sites go, with the Basilica only a short, relatively level, walk from anywhere in the center.
The church of San Damiano is located a little further away - down the hill below the Porta Nuova. Unless you really want to get in a workout you might be better advised to take a taxi down to it.

Thank you all for your help. So greatly appreciated!

I just got back from Assisi. The train station is about 4 km from the city proper and downhill. If you're arriving during regular hours, there's a bus that runs from the train station up to the city and is cheap otherwise, a taxi is the way to go. There are three churches that I really liked - the Basilica of St. Francis, the Basilica of St. Claire (Santa Chiara) and St. Rufino. I believe all three are open all day. Many of the smaller churches are only open in the morning or are closed for 2 hours or so at lunch time. Be sure to check the hours before scheduling the train.

The hermitage is known as the Carceri. It is 4 miles from Assisi, and an uphill walk. Easiest accessed by taxi.