For your entire ecosystem to float in the air, you obviously need a mechanism that keeps all the necessary components up there. Since the complex molecules that make up life are more dense than the gases making up "air" and most biological processes need liquid water which also is a lot more dense, those components tend to fall down to the ground or wherever gravity pulls them.
The most plausible way for living beings bigger than a cell to maintain buoyancy would be to feature blisters or balloons of Hydrogen.
Helium is unlikely to work since it's inert and would need to be captured directly from the surrounding air. If there is enough Helium in the air mix to capture it easily, it's buoyant effect will be much smaller. Hydrogen can be extracted from water present in a much denser air with electrolysis or some other fairly simply chemical process.
So, anything living can stay afloat, but if it's damaged or dead, it will fall down. New generations would hitch a ride on the parent until they achieve their own buoyancy, so that is not an issue.
The major problem to solve is how to get back all of the heavy molecules that fall down, out of the ecosystem.
There are two sources of heavy molecules that I can see:
- Storms/tornadoes picking up (organic) muck from the ground and spreading it into the floating ecosystem. where it's captured by large floating mats or webs that serve as a feeding ground for more complex life forms. This has the advantage of potentially cycling forever.
- Heavy molecules rain down from space. The planet/moon/ecosystem is moving through a very large cloud containing heavy molecules that somehow was blown off of a planet or escaped becoming part of a planet during the solar system's formation. This scenario would allow for a better dispersion of the molecules, but would only last as long as the cloud does, which would likely be shorter than it takes for life to evolve (balloons).
Humans would have a very hard time surviving in this ecosystem (without their own balloons/flying devices).
The first problem is that humans are heavy, with a density like water, about a thousand times more than air. They'd be limited to the biggest floating structures and risk tearing right through any spot that's too thin. Still, it is possible for a large enough bunch of balloons to support humans.
The second problem is that humans need lots of water and food to power their metabolism and especially brains, while the entire ecosystem needs to make do with very little of either.
Water would be available in small quantities from rain or clouds, but since collecting a pool of water would force a floating lifeform to sink, there are not likely to be any pools available.
Food may or may not be a problem, depending on how edible the bigger floating lifeforms are for humans. But eating the float that keeps you up there is not a long term solution. Humans would be dependent on being able to reach different floats before their food and water run out, which pretty much requires some kind of flying device, unless the number of big floats is such that they keep bumping into each other.
A more exotic way to support the flying ecosystem would be to have particles with some kind of anti-gravity effect.
It might not be pure anti-gravity but some kind of magnetic interaction (like in the movie Avatar) that forces the particles or lumps of matter containing them to rise up from the ground. This would allow for heavier-than-air materials to get and stay up in the ecosystem and would generally make it more "normal", since you just insert the needed quantity of antigrav material into any object you want and it will stay afloat. You want an island with a lake and a castle? No problem. You want a floating mountain? Go ahead.