The extra mass of Jupiter compresses its interior to a greater extent than that of Saturn. It is made of a different composition than Saturn, including a higher proportion of hydrogen compounds and rocks. Its core is much larger than Saturn's. It is unknown why this is so. Clouds form randomly, so on average there are always several layers.
Different gases are present at different altitudes in Jupiter's atmosphere.
Winds prevent clouds from forming at some altitudes, so we see clouds only at the other altitudes. Different layers represent clouds made of gases that condense at different temperatures. A massive planet exerts a tidal force on a moon that causes the moon to obtain the same rotational period as its parent planet. A massive planet exerts a tidal force on a moon that causes the moon to align itself such that its tidal bulges always point toward and away from the planet. Most jovian moons were formed out of their planet's nebula with the same rotational period as their parent planet.