(more by my own inability to predict that result rather than by Plasma/PyPRP's features)Simply put D'eux is right. To get the yellow/blue gradient we have to apply that gradient to all the shader and to do that we need to use either a vertex-painted gradient or a transparent texture, but in both cases that won't work because of the blend modes Plasma use.. The vertex colors multiply the texture colors, so the lighter parts of textures are always getting toned down and that makes our clouds go gray.. (only useful for a stormy looking sky). And if we use a transparent texture for the gradient it will only mix using regular alpha mapping which will results in washed out colors..
If we could use some additive mode then we could do something.. Using vertex colors for the gradient in the shader we could then simply add a layer with a low-contrast duplicate black and white texture of the 'base' Cloulds texture and set it to additive. That would sort of compensate for the toned down textures.
Here are some images to show the differences:
- pictures Show Spoiler
For a shader with two layers of animated clouds it would look like that:
B&W Clouds#2 texture in Additive mode (animated using Clouds#2 settings)
"Clouds#2" texture (animated)
Stencil texture for Clouds#2 (animated using Clouds#2 settings)
B&W BaseClouds texture in Additive mode (animated using BaseClouds settings)
"BaseClouds" texture (animated)
It should work.. At least in theory.
Still this is something I'll keep in mind if at some point in the future PyPRP uses an Additive blend mode.So for now we can do moving skies just fine, but without dusk/dawn effect.
I used it all over BoxAge for the light effects and sprites. Just drop in a material layer and change the blend mode in the Map To material tab from "Mix" to "Add". 
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