The Ferry is a great way to see the lakes. There is a midlake ferry for Varenna, Belliago and some of towns across the lake like Menaggio. You can reach the town of Como itself on the ferry or driving. Some ferries are car ferries but I'm not sure about parking in the towns. I'll defer that to others.
In Bellagio we stopped at Enoteca Cava Turacciolo from Rick's book for a wine tasting. We had a nice meat and cheese tray with the tasting in a old vautled stone room. Stop by there when you are in town.
Ristorante la Vista at the Albergo Milano in Varenna was great. They have outdoor seats with a amazing lake view. One of my favorite meals was there. We had Wild Deer Carpaccio, Garganelli pasta with Rabbit Ragu, Lamb Skank with potatoes au gratin, cheese and pear bread.