You'll have to do it manually.
The atmosphere desaturate the objects when they are far. So maybe you can add a level or curve effects on your layers based on their distance from the camera.
You can also achieve it with one of Andrew Kramer's presset called 3D falloff.
If you want to add smoke or fog, the easiest way is to add a solid layer, apply a fractal or a turbulent noise, add a mask with large feathered edges and animate the evolution property of the fractal/turbulent noise, with an expression like "time*100" where 100 is the value of the évolution multiplied by the current time of the comp. If it's too fast or slow, you can adjust it.
The duplicate your layer and spread them in 3D space to add depth (of course don't forget to lower their transparency to something like 10%