We stayed in Como, took the first fast boat up to Bellagio and had lunch, then the car ferry over to Varenna about 2 and walked around 90 minutes, and ready to come home - only to discover that there was only one more boat to Como that evening, and it was full. We ended up taking a boat to Menagio, then getting the one and only last boat there to Como.
We had paid $100+ for three all day boat passes too, so we figured we could come and go at will. But we nearly had to pay for another hotel night.
I suppose one should plan the entire trip out in advance, but all over Italy, I have found the people employed in the boat ticket sales industry rarely have good attitudes. Any kind of detailed discussion seems out of the question. However, there seem to be slow boats, fast boats, and car ferries. There are probably some schedules online or posted on the office wall but you have to also taken into account the day of the week and the season.