My VERY detailed report of my Sicily trip is here, including my experience with driving. It's not "hard," but it is different from driving in the US: https://community.ricksteves.com/travel-forum/trip-reports/sicily-palermo-caltanisetta-siracusa-taormina
Since Roberto says the towns you are interested in are several hours from Palermo, I would NOT recommend staying in Palermo. In addition to the commute time, driving in and out of Palermo isn't easy. So, pick up a car at the Palermo airport and base yourself closer to the towns you want to see. Of course, depending on when your flight back is, you may need to stay in or near Palermo the night before your flight.
If you don't mind being an hour or so from your towns, the agriturismo I used near Caltanisetta was a lovely place to stay.
To find flights from Rome to Palermo and from Palermo to Naples, start with Skyscanner: http://www.skyscanner.com/. If you want to book on Alitalia, I found better prices by using their International site instead of their US one. Remember that Alitalia allows one checked bag as part of the base fare, so it's not necessarily more expensive than a "budget" carrier.