@Emma188
Hi, I suggest you go to the Vatican website where you can book tickets to access the express entrance way. Bear in mind there are queues in the piazza in front of the Vatican and you have to pass through metal detectors which slows things but usually about 15 -20 mins maximum. There are many options to rent a walking tour guide through the open areas, a separate charge for one of the museums within the basilica but you can lose 2 hours easily as its vast! There is usually a crush of people wanting to get into the cysteine chapel as its surprisingly small.
We paid online to take the additional tour to visit the Popes summer palace which is using the Vatican's access to the rail line (got very confused in the underground and had to be shown which platform by some friendly guards) and entry fees and was shocked to be returned to a totally different station a long way from the Vatican and our accommodation, we were fortunate that the tiny station was expecting a train into the city in 3 mins and we managed to get tickets, validae them and catch the train! If we'd missed it we would have had to wait almost an hour for another train of bus.
Also please note water ( 2.50 for a small bottle we were told by visitors this year), drinks & food is very expensive close by, look on line for reasonably priced places on line before you visit.
It is well worth planning your visit by going to the Vatican website which is full of information and where you should get your entrance rickets as they do speed up your access enormously.
For the rest of Rome look on line for walking tour routes, you can take escorted tours or just download one you put together yourself so you get to see what you want to. Don't forget there are some amazing palaces stuffed with beautiful things easily got to by buses.
Also look for information of underground sites and tours e.g The Basilica Church of San Clemente in Rome is just few steps away from the Coliseum. Much of Italy has streets, houses, stores and passages beneath the feet of modern day life.
What ever you choose to do you won't get board and will probably need a second or third trip to see everything 
A word about safety, Rome like any city in the world is a magnate for pickpockets, bag snatchers, fake beggars who shamelessly use their children to plead with you for money (only until they are big enough to steal from you sad to say). Do not wear a back pack over your shoulder have it in front of you, never place a bag on a chair or underneath, keep it on your lap or trap the strap under the chair leg so it can't be pulled from below. Crowded busses, trains , stations, ATM's (only use those inside banks, never on the open street) & main streets are primary hunting grounds for thievery, ''Children'' under 16 are not prosecuted and the pregnant women employed by the gangs are usually released quickly. The police will only prosecute if you are willing to return to testify in court months later, so they know targeting tourists means they get off. We were followed buy two swarthy men from a church despite being 2 couples, our men folk ushered us into a jewellers and stood guard in the doorway making it clear we knew what they were about and they ran off. The jeweller also understood the situation too, so obviously not an uncommon experience, sadly.