Always put the bike inside the car if possible. The bike is safer, will not be exposed to harmful agents (bug juice plastered the paint, acid rain, rain, salt...) and your car will get much better gas mileage. Putting a bike on a roof rack will normally drop your highway mileage by about 25%. Just leaving a roof rack mounted without a bike mounted will normally eat at least 10% extra fuel. I always get a big laugh when I see someone driving a Prius with an empty roof rack fitted. Having to drive one of the most mind-numbingly uninspiring cars ever and not getting the mileage benefit.