I did a lot of research into this last spring as I was possibly moving to Vienna for six months (didn't happen, oh well). One recommendation I got from a lot of people is to 1) take a night train for longer trips, 2) avoid taking the train during commuter hours, and 3) find out if the train you want requires reservations. The only real restrictions on a Eurail pass are that 1) some trains require reservations, and 2) some charge a surcharge.
And the travel day goes from midnight to midnight--so you can change trains as many times as you like between destinations. Get your hands on a Eurail timetable (
http://www.eurail.com/1_timetables), sit down with it, and see where the trains go that you want to go.
Oh, and Rome and the Vatican are really one destination...
I don't know how train travel is in Italy, but my experience in Northern Europe was excellent.