Spoiler Warning: this page contains detailed plot
On our Earth we know that plants and animals can only survive in the troposphere - the layer of atmosphere closest to the planet that acts as a blanket. Within this layer there is enough oxygen and warmth for life to thrive. It is also in this layer that we see the formation of clouds and other weather phenomena. It is estimated that at the North and South Poles the troposphere extends to about 30,000 ft. above the Earth's surface, while near the Equator the layer rises much higher, to about 65,000 ft. We do not know exactly where on the planet Zeal was positioned, so for argument's sake let us use the lowest figure for our proof. So we can immediately conclude Zeal was raised no more than 30,000 ft. (about 5.6 miles).
Next we have to take into consideration the type of weather that was occurring during the Dark Ages. As the planet was consumed in an ice age we see severe storms batter the surface. Snow, ice, rain... all types of precipitation were present. From this we can conclude the clouds that were in the sky during that era were stratus clouds, as they are the type to produce such fierce weather. More precisely we can say the clouds were nimbostratus, known for their dark grey ominous appearance. Stratus clouds usually form in the atmosphere at altitudes no higher than 6,500 ft. When Crono's team is teleported to Zeal we can look down on the cloud layer and see a thick blanket of clouds, typical of the nimbostratus type. Thus we can conclude that layer of clouds is no more than 6,500 ft. above sea level. Though it is possible for it to have formed much closer to the surface, we will use the maximum height for our calculations. If we were to use the lowest (around 50 ft.) we would find Zeal to hover only a stone's throw above the surface.
By looking at Zeal we can determine the islands float even higher than the tops of the cloud cover, as we are able to view them from above. Because it is difficult to judge depth on a television screen we cannot be certain as to how much higher Zeal is than the storm clouds. We might assume there is at least a 500 ft. difference between them, but it may in fact be much be higher. As a result I have concluded the minimal elevation of Zeal must be around 7,000 ft. If you prefer you can add more distance until you come to a figure more to your liking. Though I would suspect Zeal floats no more than 10,000 ft. above the Earth's surface, which is just shy of 2 miles (1.89 mi. actually). So in summary we can conclude the following:
Clouds < 6,500 ft < Zeal
< 10,000 ft
These results are perfectly understandable as it is known humans are capable of surviving at such altitudes. Once one has become accustomed to the initial change in elevation, he can find a comfortable existence residing on the floating continents of Zeal.