I'm assuming you want to maintain paralax shifts with camera moves for objects in the background between the sky and the Horizon layer.
Here's what you do. Set up a comp tall and wide comp with your 3D background elements distributed in 3D space. Take your background image, the one you want to use as a sky for example and put it at the very back of the composition then scale it up so that it fills the frame.
Now drop that tall and wide comp into a new standard sized composition, collapse transformations, and then add a new Comp Sized solid to the comp and appy Effect>Trapcode>Horizon to the solid. Choose your tall and wide comp as the source for the Image Map, adjust the H and V coverage to fit your project and add a camera. Everything should behave as expected. Horizon will see through the tall and wide comp and read the scene as a 3D world centered at the comp world center.
Here's a CS6 project just using shape layers, a solid and a grid to get you started. Open it and move the camera around a bit.
I apologize the thing I'm trying to do is a little difficult to explain.
I want to render out a spherical map to use in Trapcode horizon. Specifically, it would be a space scene with stars, nebulas, and 3d asteroids. I want to be able to build the scene in After Effects (which would be a completely 360 degree scene) using Element, Trapcode Form, Particular, shine, etc.
I'd render that scene out as a spherical map that's 16000x8000 pixels, as a PNG or whatever, and then reimport that into AE for use in Trapcode Horizon. That way I don't need to keep rendering the scene in full 3D (since all of that stuff would be an infinite distance away).
Again, Cinema4D allows this by baking out the reflection map of a sphere put in the center of the scene. I just want to be able to do it in AfterEffects since it's easier to do lighting effects that I want and use stock photo layers.
Horizon will take anything you build but if you render some scene that you build you will loose the 3D elements because video is flat. Horizon will give you the ability to pan around the universe with your camera but the universe will not be 3D unless you set up 3D layers in a pre-comp and use horizon to 'bake' your 3D background.
I'd just build 2 or 3 big stills, make a new comp with them and then distribute them in 3D space, pre-compose and use horizon. That's your only solution. It's just like saving texture maps or environment maps in c4d.