I like having the cover on mine. Keeps warm engine air out and keeps the filter cleaner. If you are worried about flow, don't be. The S&B kit not only receives air from the front inlet, but also from the fender.
When I ran the 6637, I had an issue with a mold/mildew type material on the paper filter. Any water that would get between the hood and fender would end up on the filter. That was my biggest complaint with it.