I would just do transfers and then book the specific sites you wish to see for each city. For Rome, you can easily take the train to and from the port. It's very easy, fast and cheap. Once in Rome you can easily get around the city by walking, metro, bus or taxi. There are really only a few sites in Rome that you would want to book ahead in order to bypass the lines, the colosseum and the Vatican museums, so if you plan to visit those be sure to book as soon as you can. You can also book tours of both sites but be aware that if you do you won't have much time to visit any other sites in Rome.
Donna