Jupiter is mainly composed of hydrogen and helium, all the other gases are in trace amounts. It is those gases in trace amounts that give the different colors.

Helium and heavier gases are indeed pulled closer to the center of the planet, because of gravity. But they nonetheless form a sphere, because that's the shape that minimizes the gravity pull.

There is still helium on the outer layers of Jupiter though, because helium is a gas. That means that helium atoms are moving around really fast and have a lot of kinetic energy, so even if gravity pulls them towards the center of the planet, some atoms still manage to stay in the outer layers. And contrary to some liquids that you cannot mix together (oil and water), gases mix together very well. The same is true for other gases. Solids, on the other hand, have fallen towards the center of the planet, so we cannot observe them, even though we still think there must be some rock and ice at the very core of Jupiter.