You should apply for a visa from the country which is the main destination of your visit.
If the main reason for your trip is a conference or a business meeting in France, and you incidentally want to spend some time in Switzerland, then you should apply for the visa from France.
If however there is no more reason to visit one rather than the other (for instance if you're just visiting both countries for tourism), the rule is that you should apply for a visa from the country where you intend to spend most of the time in (which would be Switzerland in your case).
Short stay visas allow you to travel to any other Schengen Area country during the validity of your visa, so you can indeed travel through France on your way in or out of Switzerland (or vice-versa).