The guide I read said open unlatch the roof, then put a sheet or something under the roof covering the body work.
Personally I didnt bother. I just sprayed it straight on and used a newspaper held in the other hand against the bodywork top prevent any getting on the bodywork. If any went on the glass I wiped off immediately and then later polished up all the glass anyway.
I also didnt worry about how thick i sprayed the stuff on. It all looked a bit strange when it first goes on the roof, but dried perfectly and left no streaks or spray marks.
+1 i just had spare cloth and wiped off over spray just make sure you get even coverage and will be ok