My 2 friends and I booked the 12 night repositioning cruise on Navigator of the Seas and had a wonderful experience.
We took the train from Rome to the port thanks to advice from fellow CruiseCritic.com members and find it to be a relatively easy process. Be prepared for the 10 minute from train station to the port entrance.
The check-in process at Civitavecchia was quick. Our room was ready when we got there at 1:30. Our room steward was very efficient and he also made us towel animals for the last 5 nights. Room was spacious enough for 3 people and we were able to hang up or store most of our clothes. The location on Deck 2 turned out to be great since it was quiet and close to the disembarking area located at Deck 1 below. The only thing to be aware of is that you can't walk through the whole ship on decks 2 and 3.