Best way to navigate Rome in a short time

I would use the hop on/off bus,

Ditto Frank's recommendation of the Hop-On, Hop-Off bus. It's particularly good for the first day when you're jet-lagged, since it requires no planning, reading of maps, figuring out of transit systems, etc. Stay on for one complete circuit, then you can decide where you want to get off (or if you just want to quit after the circuit is finished).

Is this something you have to book ahead of time or wait to we arrive in Rome?

I, personally, don't like the Ho/Ho buses. I would just grab a good map and use a combination of walking and the metro. This way you can spend as much or as little time at each site and leave when you want without waiting for the next bus to come. Donna

The advantage to a HOHO bus is that they're specifically designed to take you to the major sites. The drawback is that they're kind of pricey. The drawback to taking the Metro is that you're underground and you're missing getting to see what's between the sites that you're going to. The advantage is that it's cheap. Ron In Rome has an excellent summary about the HOHO buses here: Hop On Hop Off Buses in Rome It's worth your time to follow that link. (For instance, I didn't know that the HOHO routes have been scaled back quite a bit since 2010.) Happy travels.

You buy your ticket right at the first bus stop, or sometimes they collect the fare on the bus. You can ask at your hotel desk where a stop is located. I am one who likes the hop-on/hop-off bus tours as a great general overview of the cities. I see where things are located and figure out which ones I want to go back to visit in depth during my visit. They have them in all major cities (seems like all over the world.)

Where are you staying in Rome? Personally if I had an afternoon before meeting the hordes and after checking in I'd head out the front door and explore the surrounding neighborhood. Where can I get coffee, some fresh fruit, bus top, metro stop etc. Since you'll be guided on the tour the majority of the time wander and explore. Then again it's fun to turn the corner and see the Colosseum looming in the distance. For a useful map use the satellite image option in Google Maps. In the search box type in Colosseum Rome Italy. Hit enter. When the map appears click on Satellite in the right hand corner. When that image appears use the zoom on the left. Keep clicking on the + until you have a bird's eye view of the Colosseum. If you have the exact address of where you are staying click on the Get Directions box in the far left corner, type it in, click on the little person for walking directions or the bus for public transport (sometimes this can be confusing) and hit Get Directions. Lo and behold a route to follow. I use a Mac so I am able to do a screen capture of the image and print it out. Oddly if you just hit print the satellite image doesn't print out. The map does but not the bird's eye POV. I find looking at a city this way gives me a good sense of perspective i.e. how close or far sites are. As I like seeing a city on foot that's how I saw Rome. Even did the mile trek to the Vatican. Have a wonderful trip.

I agree with Claudia, and if you do get tired, taxis are reasonably priced. We were there in March and a taxi from the Vatican to the Pantheon was €7.