amatula,
With the starting and ending points of the tour, the easiest solution would probably be to use open-jaw flights, inbound to Munich and outbound from Geneva. You could also use Zürich, although you'd have to get there from Geneva by train, which is about a three hour trip direct to the airport.
You could also consider an inbound flight direct to Salzburg, although that would likely involve a short layover and change of planes in Frankfurt. I'm not familiar with flights from your area, but I'm sure one of the others will be able to provide more specific information. You might want to use a Travel Agent just for the flights, as I'm sure they'll be able to find the best price.
If you decide on using Munich, it's very easy to get from there to Salzburg. The Germany experts on the forum can provide all the options, but the route I'd use is to take the S1 or S8 (S-Bahn train) from the airport to Munich Hbf (main station) and then a direct train to Salzburg.
At the conclusion of the tour, I'd suggest using one of the Shuttle Vans from Chamonix to Geneva Airport (I can provide a suggestion if you're interested). That's by far the easiest and quickest option.