As has been stated, check the sealants around all the items on the roof, reseal as needed. Washing the roof once or twice a year will help keep down the black streaks down the side. A little dish washing liquid, bleach will do wonders on any roof type. If a rubber roof, most manufacturers will tell you no protectants needed or recommended. You will also want to check the roof AC to make sure the seal is tight. There are usually some (4) bolts that should be checked/tightened from time to time to make sure the gasket is providing a good seal.
Tom Wilds
Blythewood, SC
2016 Newmar Baystar Sport 3004
2015 Jeep Wrangler 2dr HT