Well, I don't think CloudWright is the right tool for the things you want to do, unless you want to prerender the skies. CloudWright is (only) for cloudboxes I think, unless it has changed since the last time I've tried it out.

DarkClouds on the other hand, can do most (if not all) of the things you've mentioned there.
- you can change teh color of the sky ('DC SET SCATTERING Red, Green, Blue')
- 'DC SET CIRRUS IMAGE Image Index' allows you to change the image for the cirrus clouds (high altitude)
- the direction the clouds move can be altered by changing the wind direction
- you can alter the density of the clouds from 0.0 (clear skies) to 1.0 (overcast), and have rain falling
- and you should be able to change the night/day cyclus too, by adjusting the time of day...
- there's also the ability to change the sun color, the lensflare image, add moons and planets, etc...
Cheers
SLAYER RULES! YEAH, MAN!!