Best way to travel in Rome?

[Em M's mom]

My family of four - one being a baby - will be getting to Rome on a Monday and staying until Wednesday. We are staying near the Vatican Wall, but of course we want to see everything. Whats the best way to travel for those few days?

Also, we are taking the train to Pisa on Wednesday, is the train pretty easy to figure out?

Then in Pisa, whats the best way to get around. We are staying in between Pisa and the airport.