I would stay overnight in Milan near the Central Station. Then the next morning I would take a train to Florence and then one to Arezzo. I would rent in Arezzo. Avis has an office across the street from the Arezzo station, and all others, like Europcar and Hertz, are a short taxi drive away.
From Arezzo to Cortona is a 20 min drive.
Normally I would recommend to drive all the way from Milan, but you are traveling in winter, and if it's foggy in the Po Valley (it often is in winter), or if it is icy on the Apennines (Bologna to Florence) it's not going to be a fun drive.