If you take the C30 bus from Bellagio to Como San Giovanni train station, I have some additional info. (We took this bus last May.) You can buy the bus tickets at a place close to the ferry dock in Bellagio. It is not a tobacco shop, maybe a bar. Nonetheless, there is a sign in the window that says they sell bus tickets. You should stop here when you arrived in Bellagio to find out the bus departure times. The bus stop is also right across from the ferry dock. The ride is over an hour, and be sure to sit on the right to see the lake from the bus. San Giovanni is a ways from the dock and the center of Como. Then you are faced with purchasing train tickets back to Milan.
Since this is a day trip from Milan, it might be easier to take a regional train from Milano Centrale to Varenna-Esino train stop which is an hour. Walk to the ferry dock, following signs. Ferry to Bellagio and explore this village (peruse Rick Steves Italy book and focus on the section on Bellagio). Return to Varenna and walk the lovely promenade. Maybe take a mid lake boat tour in the Varenna Taxi boat. They also include a tour of Villa Balbianello in one of their tours. Return on the regional train back to Milan. This region of Lake Como is very picturesque. You may not miss seeing the village of Como.