I have a 2001 Haulmark enclosed with a flat one piece roof, what is the best thing to coat it with, I have heard people say the silver mobile home roof topping, but I am concerned about it staining the side's when it rains, any Idea's???

Liquid EPDM should work. Most RV suppliers or home building centers will have a form of coating like this one.
I did the entire roof of my truck camper 2 yrs ago with EPDM pond liner from Home Depot. Cost less than $200 to buy a 15 ft length 8 ft wide and glue it down to the roof structure. No leaks so far, but I will be coating it with the white liquid this year, just for UV protection.

http://www.epdmcoatings.com/whyepdm.html

Go to an RV dealership and buy some of the white rubberized roof coating. It does not crack, that I have seen. The silver roofing will crack but does not run. A 2001 should have a rubberized roof. I would not be to worried about it unless it already leaks. Come to think of it, I just pulled one of those trailers and I thought it had the rubber roof.

no leak's that I have noticed, I am just concerned about where it comes over to the edge, there is some sort of grey sealer there and there appear's to be areas where they didn't get it sealed well (gap's, pin holes and such)