Travel from Lago di Como to Munich is basically going to be a fully day, so I'd suggest using the shortest travel time possible. One of the shortest on that route is this one....
- 07:37 Depart Varenna-Esino
- 08:38 Arrive Milano Centrale
- 09:05 Depart Milano
- 10:27 Arrive Verona Porta Nuova
- 11:02 Depart Verona
- 16:24 Arrive Munich Hbf
If you're staying in Bellagio, you will of course have to be up very early to take the Ferry to Varenna and then walk up the hill to the station. There are similar departures at 10:37 and 13:37 but my preference would be to take the earlier one as it gets you to Munich at a decent hour. One other advantage of the 07:37 departure is that you'll be travelling through the beautiful Brenner Pass in daylight (between Verona and Munich), a trip I always enjoy.
The trip from Munich to Berlin is very easy. There's a direct ICE departure (no changes) at 09:16, arriving at 15:20 which is the one I'd use. If you need to buy tickets in Munich for the trip to Berlin, try the EurAide office which is (as I recall) at desk 1 in the main ticket office (to the left as you go through the door). They have English speaking staff, and are very helpful.