I suggest you get John Hermann's book, Motorcycle Journeys Through the Alps and Beyond, it is the Bible for riding in the Alps. Be sure and ride the Dolomites along with the Alps. You will need a vignette (toll) sticker to ride the motorways in Switzerland, they will be available at the Swiss border and speeding can result in a very pricey ticket. You should get familiar with the road signs and since you will be in France learn some of their unusual rules of the road along with how to navigate traffic circles, using your turn signals is the key.
Since your starting in Lyon, ride the Route des Grandes Alpes and Route de Napoleon, there are also some amazing roads in the national parks along the French and German border. From Lyon you are also near the Pyrennes at the border of Spain and France, that area is great along with the Picos de Europa in Northern Spain.
I have not stayed in Andermatt, there are so many small B&B's in Europe to choose from.
'16 BMW R1200GSA
'15 BMW R1200GSA - totaled
'13 BMW K1600GT
'08 Suzuki DR650