mex,
On that route, I'd suggest using ground transportation rather than a flight. As the others have mentioned, you'll first have to get to Zürich airport, then go through the usual routine of check-in, security, waiting, boarding and deplaning, flight times (with possible delays) and then transportation into your destination city. You'll also have to contend with cramped seating, expensive and restrictive baggage limits and the usual air travel hassles. It will be a grueling trip that will take the better part of a day.
As Sam mentioned, one of the easiest solutions will be a train/bus combination. Using Interlaken Ost as the departure point, the quickest trip will be a departure at 07:29, arriving Munich at 13:29 (time 6H:00M, 3 changes, last leg via bus). The train changes in Bern are very straightforward. The transfer to Bus in Zürich is also easy although there's a short walk..... the Carpark Sihlquai is visible from the station, across from the entrance to the Hotel Walhalla. You should be able to walk there within five minutes.
As I recall, the Hackerbrücke central bus depot is close to the Munich Hbf, but behind the main entrance. It shouldn't be difficult to get from there to your hotel. Depending on the location of your hotel and as you'll have luggage, you may want to use a taxi.
If you're going to be using the Hbf during your visit, I believe there's some construction going on there at the moment, so there may be barricades or other activity in certain parts.
