Fast answer
A good Menaggio ferry day starts with the route that must work, then adds optional stops only if the timetable, tickets, weather, queues, and final return leave enough slack. Bellagio and Varenna are different decisions: one is the classic central-lake pull, the other is the rail-side crossing. Cadenabbia matters when the car ferry or Villa Carlotta side changes the plan. The safest first version keeps the day narrow.
If you only do one thing
Pick one main ferry target from Menaggio, then add a second crossing only after the final return, ticket type, route, weather, and queue pressure are clear.