Dbone,
Since you're taking the trains here's a couple thoughts.
Don't take the super fancy 'high speed' train. It's more expensive and yes somewhat fancy. You can buy a sandwich on these for about $12 and a coke for $5. They are totally enclosed and air conditioned. Boring.....
Take the city trains. Now this is what Italy is about! Windows open, curtains flapping at 80 mph, and when another train passes the other way you get a tremendous wind blast. You'll go through some incredibly long tunnels also.
It's a lot of fun seeing the people and generally fitting in, in a tourist kinda way. Take a bag with your drinks and munchies.
*The trains run absolutely on time so don't be late.
Rule #1
Remember that nobody speaks English in the train stations so do your research on what trains to transfer on towards your destination. Yeah, you'll go into the Rome Station and ask for a ticket to Bologna (or Borgo Panagiale if a train goes there).
The surly state employee ticket guy in the cage will mutter inaudibly in Italian about your ticket with absolutely no interest that you are obviously a tourist and don't know which end is up.
Rule #2
The tracks are called Binaria. #1 through whatever. Simple enough. But.........
In some of the larger cities there are two separate levels of tracks. Both are numbered Binaria 1 through say 12. You look on the reader board in the station and say yup, my train is on track 7. Your tickets may say Binaria 7, but not which level! So be sure to figger this out. Now how did I know this?
I missed a train due to this error of mine but fortunately I discovered my error and caught the next one to Roma.
Before you leave home study the Italian names for cities.
Florence = Firenze
Venice = Venezia and so on.
Roma=Rome
Other city/town names we take for granted will be spoken and spelled differently when you see them in the stations and if you are on the road.
Case:
I asked someone for la treena (train) to Florence and I got a perplexed I don't know where that is look. Then I remembered to say Firenze and all was well.
You'll have an absolute ball. Just take a lotta loonies as things are expensive by our standards.
edit:
It's been about 5 years since I was in Italy. Are you sure there is enough time to leave Rome in the morning, go to Borgo Panagiale, do the museo, knock around for a few hours and back in one day?