Driving via Pontarlier is the best route. If you want to stay overnight drive untill you want to stop then find a Formula 1 hotel, there are plenty around on the major roads. As mentioned to drive on Swis motorways you need a pass, which they force you to buy if you go over a main motorway border. I think it was 40 euros last year. You could drive via the non motorway but that means driving around the edge of lake Geneva, which trust me, is a nitemare!
It depends on if you like driving, but me and the parents tend to fight over the driving, as it makes the journey less boring, but it means its very easy to do in one go. We normally get a evening ferry then drive through the night with a short in car sleep and arrive around lunch time.
P.S. From past experience the best way to get up the twisty road to Verbier is in a Aireal Atom … beats any biking out there! It was about 20 times quicker than my fully loaded Hillman Imp!