Depending on how they collide,either the mass of the moons would be combined with Pluto, or there would be a massive ejection of matter away from the surface, some of which could escape the Pluto-Charon gravity and become asteroids or meteors, and some would become an orbiting debris field. It would not alter the atmosphere, except there would be a lot of dust in the air. I imagine its appearance would be a lot lumpier looking than at present.