You could have what you want in different scenes, and then combine the render result of each of them in compositor. You can even combine scenes from different render engines.
You suppose that you can render a sky in Eevee much faster than in Cycles, so in one scene you can render the sky with Eevee and combine it in compositor with the rest in Cycles:
Scenes_compositing.blend (1.1 MB)
Here I have used very last Blender 2.8, you may need to download the newest one from buildbot. I used this shader in the example:
https://blenderartists.org/t/procedural-cloudscape-generation-in-cycles-now-eevee/694700