We hired a car here 2 times, both were very good but this last time was amazing thanks to Tao. He gave really good instructions and an excellent service.
The only problem we had with our car was that one proximity sensor was beeping all the time no matter what we had in front, but luckily we could turn it off.
You can go through tolls in France but you need to buy a sticker for the Swiss tolls.
To find the counter in the french sector inside the airport you have to go to departures and at the end of the check in counters (we took some mechanical stairs and it was to our right), there is a super small sign that says french sector. Then you pass french customs and you'll arrive at the car rental sector.
To return the car we filled the tank at the Carrefour in Ferney Voltaire that is 5 minutes away from the airport.