You can use pipe insulation to pad the arms of the rack and bungee cords or velcro wraps to attach bikes to rack. I went to the sporting goods store and bought some foam blocks that are designed to allow you to carry a canoe on your car roof. They are about 4" square cubes, with a slot cut in one side that connects to a tubular cutout. They work great to put wrap around a bike frame tube wherever it might touch the rack or the vehicle also.
If you have an REI nearby, they might have the canoe carrier blocks.
