I wouldnt put car cover on a wet car or a car that hasnt been washed, I think that If you do you are risking some scratches and/or swirl marks. This is just my .02$
The cover is to prevent your car from being rained on. It sort of defeats the purpose if the car is already wet, eh? You never want to put a car cover on a wet car because the water will fail to evaporate correctly and the water spots will be a major pain. Not to mention that if the sun comes out right after it rains then it could get pretty humid under that cover and your cover could get a little moldy or something. Only put the car cover on if the car is dry and clean. It saves you swirls and other damage. Not to mention that your car cover will be more effective if the underside is kept dry and dust free.