Option 1: Density (water and air)
Option 2: Polarity (oil & water)
Density is the most straightforward hard-science approach. You would have a first layer of life at lower elevations, and another layer of life at the higher elevations. This is actually exactly what we have on Earth, where we call the boundary of environments "sea level." The only difference being the two environments in you world are both gasses, rather than one liquid environment and one gaseous.
The other option is that one of the gasses exerts polar (electromagnetic) waves, and the other doesn't, you would have pockets of each gas cluster together, like attracting like, and repulsing the other. This is why oil & water separate. Water is polar, and attracts itself. If you leave oil & water in a container they separate with oil on top because of density, but the initial separation is due to water's polarity. If they were the same density, you would get something that looked more like a lava lamp.
Now, perhaps the planet did not have enough gravitation such that both gases tend to escape, or perhaps the two races are competitively colonizing an environment that had no existing atmosphere, so some sort of handwavium-based technology could initiate a new "pocket," or hold pockets together. You'd then have something resembling blobs of mercury on a table, with empty space in between.