One good thing about having a cover over the Beast is that I don't have to deal with it getting as dirty/yellow as before and the pretrip wash is soooo much easier.
My prior SOB had a rubber roof, the Beast is fiberglass so it has been awhile since I've had to deal with it the same way. Here is a link to an article on
Rubber Roof Care that might help with the understanding of the black spots. I found that keeping the rubber roof clean also helped the side walls stay cleaner longer. One of the thing I like about the older Excels is the 'gutters' that trims the roof/sidewalls.
I just washed the roof with soapy water and used brushes strong enough to clean the surface. As far as the black spots I've used a mild bleach solution with soap to reduce the staining. Still use it today to remove staining on the fiberglass. Sometimes I used a commerical cleaner/treatment but didn't notice a difference and if I remember correctly, Dicor stated it wasn't needed. I'm sure there are as many approaches that work and recommended.
Being the third owner of my unit...and I'm sure they never waxed it before...I'm now in the Cleaner/Wax phase when I wax/polish the unit. I've experimented with several brands but use Meguires.