If you are heading to any mid-lake destination (Bellagio, Varenna, or Menaggio) on Lake Como from Milan via train, catch the one hour ride to Varenna-Esino via Lecco. We were told by a TrenItalia representative that this train would be shown as "TIRANO" on the big board at Milan's Stazione Centrale, but it actually appeared as "LECCOTIRANO" and we almost missed it. So be sure to double check the train number on the monitors located at the head of each track. You can also reach Bellagio from Como, but you will be in for about a two-hour ferry ride; in comparison, a ferry from Varenna to Bellagio takes less than 15 minutes. A one-way second class train ticket from Milan to Varenna costs a mere ITL8,100 (about $4); first class is ITL12,200 (about $6). A one-way ferry ticket from Varenna to Bellagio costs ITL4,800 (less than $2.50).
There is no ticket office at the Varenna-Esino station; you can, however, purchase a train ticket to a short list of destinations, including Milan, from a vending machine at the station. But if you are headed elsewhere from Varenna (for example, it is possible to take a train to Tirano and catch the Bernina Express to St. Moritz, Switzerland), you'll need to get a ticket from the travel agency in Varenna, I Viaggi del Tivano (Via Esino 3, telephone +39 (0)341 814009, email sberet@tin.it). Just walk from the Varenna-Esino station down the hill towards the waterfront; the travel agency will be on your right next to Albergo (Hotel) Beretta. The people at the agency are friendly and speak very serviceable English.
If you want to venture beyond the three mid-lake villages, Lugano, Switzerland is a worthwhile day trip. If you don't have a car, to get to Lugano you'll need to take a ferry to Menaggio and buy a bus ticket at the newsstand in the center of town. Our hotel had the bus schedule. The bus stop is a couple of blocks up the hill from the newsstand. It's about an hour ride across scenic views to Lugano. I Viaggi del Tivano in Varenna has walking maps and tourist info for Lugano.
They say hindsight is always 20/20, and if we were to do it over again, we would rent a car at Milan Malpensa and drive to Bellagio rather than rely on the trains, ferries, and buses that serve the Lake Como area. This will give you a lot of flexibility if you're going to venture outside the mid-lake region (to Lugano, for example) as we did. Otherwise, the ferry, train, and bus schedules will almost certainly leave you waiting somewhere along the line. You can get your car on a ferry with ease if need be.
We felt two days in Bellagio was plenty of time for us to relax and unwind after stops in Milan and Florence. Add a third day if you want to include the day trip to Lugano.