I have been using rex textures for everything. I know some people have mentioned HDEv2 for clouds. For those of you who have used Rex textures have you switched to other textures with better results? If I were to try another set of textures, for example HDEv2 then would I end up losing the rex textures for runways etc, or is it possible to have one set of non-rex textures for clouds and use rex textures for runways? I am looking for a texture set that would go best with active sky next.

You can use whatever kind and mix of textures you want - just like always.  Just find the replacement textures and overwrite them in the correct directories for what you want to replace.