I don't see the logic of flying ZRH-MUC then taking the train to Berlin?
If there isn't a specific reason for this I would either fly the entire distance or train the entire distance. You can get a night train from Zurich to Berlin - not daily, departs 7:44 pm, arrives 7:18 am.
Check the German railways website:
www.db.de - it is excellent, and available in English.
Audrey