We were there last week for just a couple nights in Tremezzo (just across from Bellagio on the west side of Lake Como). That portion of our itinerary included the following:

1. Arrival into Milano Centrale train station by train from Venice.
2. Metro subway from Milano Centrale to Milano Cadorna train station.
3. 1 hour train ride (departs hourly) to Como Lago station close to the ferry port.
4. Fast ferry to Tremezzo. (Approximately 1 hour.)
5. Ferries next day to Bellagio, Lenno (Villa del Balbianello), and back to Tremezzo.
6. Returned next day to Milan by ferry and train.
7. Stored luggage at Milano Centrale. (Luggage storage office was closed at Milano Cadorna.)
8. Saw The Last Supper and the Duomo with local transportation by Metro.
9. Airport shuttle bus from Milano Centrale to LIN airport. (4 Euros)

There are several train stations in Como. The station within close walking distance of the ferry port is served by trains from the Milano Cadorna station. A short taxi ride from the Como station served by trains from Milano Centrale would probably have been perfectly suitable. We did not spend any time in Como beyond our connection time between train and ferry.

Villa del Balbianello was definitely worth a visit. We didn't find Villa Carlotta as interesting, but the gardens are beautiful. In Bellagio, we enjoyed lunch in the courtyard at Antico Pozzo. (Up the hill. No lake view.) On their website, see their "How To Get Here" info for a decent overview of some other transportation options such as a train to Varenna.

I have Lake Como ferry schedules/pricing/opinions available if and when you need them. The ferry schedules all looks more complicated than they really are. I have copies of this past summer's schedule. The winter schedule just began last week.

Here's another site with good public transportation info.

I can't imagine wanting a car there all week, but I guess that it depends on how you arrive, exactly where you stay, and what types of side trips you may wish to take away from the Lake.