It depends whether you travel before or after March 29.
Before March 29, GVA is outside Schengen so you will stay in the international zone at AMS and clear immigration and customs at GVA. Your bags will be checked straight through and come out on the same belt as other passengers from AMS.
From March 29, GVA will be part of Schengen, so you will clear immigration at AMS. However, as Switzerland is not part of the EU Customs Union, you will have to go through customs at GVA (as will all passengers from AMS). Note this is totally painless. Collect your bags with those from all the AMS passengers.