I just bought some stuff from the SPCA called 'Eliminate' which uses enzymes to break down and get rid of the smell. You can use it on upholstery as well as lots of other types of materials (I'm using it on the tiles in my garden) so you should be able to use it on the floors and seats in your car. Maybe you could try something like that. I have seen similar for sale in other pet shops. Not sure how well it works though.
Clean the dog? So you don't get a smelly dog to start off with.