You will need to research booking tickets to see the Last Supper. They only release a few at a time and you will want to be ready. We saw two years ago and it is a special experience.
For the Cinque Terra I would stay in Vernazza or Corniglia. Get a ferry pass and go from town to town as well as walking where you can and taking the train. I would stay two nights if you can.
We stayed in Bellagio on Lake Como. It is central and and interesting town. We wanted to stay in Varenna but our accommodation was cancelled. It is quieter and close to the train station. I would stay at least two nights. We spent three, but made a day trip by train to Milan to see the Duomo and the Last Supper on one of the days.
For Tuscany I would recommend a car. I have been several times and have only scratched the surface. Siena is wonderful. We spent two nights there and it is a good base for seeing much of Tuscany.
Edited: 12:32 pm, May 28, 2013