miofgreen,
It might have been better to start your own thread on this topic. A few comments on your questions.....
To begin with, forget Rail Europe! Their prices are often higher than purchasing from the rail networks or other sites, and they don't sell tickets for all routes.
If you're only travelling between the three cities you mentioned, you'll be using the high speed trains, either Trenitalia or Italo Treno. You can use either rail network on those routes, however one point to mention is that Italo Treno sometimes uses a different station in Rome (Roma Tiburtina).
You can purchase the tickets for either rail network at Captain Train, often at considerable savings (depending on how far in advance you purchase). However, it's important to note that those trains have compulsory seat reservations which are specific to train, date and departure time and can only be used on the ONE train listed on the ticket. If you board the wrong train by mistake, you'll be subject to hefty fines which will be collected on the spot.
Before boarding the train, check the electronic board to determine which track no. (Binario) your train is leaving from. Your train number will be shown on the ticket (ie: AV-9718). Your tickets will specify a Car No. (Carrozza) and Seat No.'s (Posti), and you must sit in the assigned seats. You may find it helpful to watch THIS short video tutorial. If you place larger items on the luggage rack, as shown in the video, keep a close watch on them so they don't "disappear" (I've had some "close calls"). Smaller carry-on size items can be placed on the rack above your seats.
One other important point to mention is that if you'll be using any Regionale trains, Buses, Metro or other transit, you MUST validate tickets prior to boarding on the day of travel, or again hefty fines! In most cases, validation is accomplished by inserting tickets inside the track side machines and getting a time & date stamp. If riding the Vaporetti in Venice, this is done electronically by "tapping" the ticket against the reader. If you get a green light, you're good to go. If you're going to be travelling by train from Rome to Civitavecchia to connect with your cruise, you'll likely be using a Regionale train, so you'll need to keep that in mind.