I would pretreat the roof with a product such as Opti-coat which would prevent you from having to wax the vehicle in the future. With racks in the past I always used a pressure washer and rags to clean the roof. Some people have to use a long type brush. But if you pretreat it with some type of polymer treatment and keep it clean it will prevent any issues.
I have been working on a solution from this since I went wheeling a couple of weeks ago and have not been able to get all of the mud with a pressure washer.