I just had a stage one put on my bike and kept it open with one of the covers. I got the rain sock barbecue i do ride in all weather. I wondered if i need to cover the cleaner with a bag or if the rain sock will do when i wash the bike. I normally use s1000 to clean it, but when i do a pull wash will the suds get through the sock.
I use plastic bag from the grocery store or target anyplace like that. I just pull it over the heavy breather then tie the handles. Works great and cheap. I save the rain sock from rain. That's just me though.
I have done it both ways, naked and covered. The biggest problem is when it is not covered it seem to drip dirty water on my chrome cam cover for a long time. Even if I blow dry it still drips. I hate the drips.