If you are going to Sicily after visiting the mainland, you can either take the train or drive. The trains drive right onto the ferries, so if you don't want to, you don't even have to get out of your seat (but the views topside make it worth your while!). If you're driving, you'll find that the ferry service to Sicily is one of the best organized things in Italy. There are public ferries and private ferries. The public ones cost slightly less than the private ones (but both are inexpensive). Both take cars or walk-on passengers, are easy to find in Villa San Giovanni and Messina (just look for signs with pictures of boats and the word "Sicilia" on them), and leave every 15-20 minutes, 24 hours a day. No advance reservations are accepted, but except in August, you will rarely have to wait in line to get on.
From April 20 to October 7, you can also take a ferry or hydrofoil from Naples to Palermo. Either one takes cars. The hydrofoil takes four hours; the ferry leaves at 7:30 and arrives the next morning. Onboard services include amusement arcades, TV, movies and even a discotheque! The same company also runs a hydrofoil to Lipari in the summer.