Take them off!!!! But only if you don't have the wheel arch things either!!!
I had to take mine off since my wheel/tire combo would not fit with the mudflaps..LOL. I love the way it looks. and my paint is flawless.
http://img.photobucket.com/albums/v5...0Nice_View.jpg
http://img.photobucket.com/albums/v5...ndra/angle.jpg