Getting to either place is easy from the port. You can read the "train travel in Italy" sticky post in this section for details on how to do this. Its easy. You can swap from train to subway in Rome at the same train station and be within a half mile of the Vatican from the subway station. The Colisseum is across the street from its closest subway station. If you buy a all day train/metro ticket (ask at the train station in Civitavecchia) you can just use the trains to get back and forth.
For tour guides, we just did the self tour with Audio guide at the Colosseum (see the other recent post about this) but you can also pay for a tour there. For the Vatican, you can also just go in on your own (its free to go in but to see the museum portion there is a fee) or you can barter with one of the many tour guides out front. Be careful here, they will overcharge you in a heartbeat if you let them.
Carnival Cruise Lines:
Fantasy 90, Celebration 95, Victory 05, Conquest 05, Spirit 6/06, Freedom 6/08, Holiday 7/08, Victory 6/09, Valor 9/09, Dream 6/10, Splendor 8/10,Conquest 8/11,Magic 11/11,Triumph 4/12,Spirit 7/12,Freedom 11/12, Triumph 2/13 - The fire cruise
NCL Dream October 2006, RCCL Mariner OTS June 2007