@aerthi
I'm not sure you can, not at the same time anyway. You can change the colour of the clouds to be different depending on different times of day, but I don't think you can apply multiple distinctly different colours to various parts of the clouds at the same time, just slightly different gradients of the same colour (darker/lighter etc) that are caused by the darker/light areas within the textures in 'v_clouds.rpf'.
If you've seen any screenshots of mixed colour clouds, post them here, I might have an idea of how they have been created if I see screenshots of them, but I'm pretty sure it wouldn't be possible using 'cloudkeyframes.xml' alone, it only has values that apply the same colour to the entire (3d looking) clouds all at the same time.
You can contrast them by changing the colour of the background (simple) clouds. Their colour is controlled within the timecycle files. Other light sources like the Sun/Moon influence the perceived colour of clouds within their area of influence & certain fog colours within the timecycle files likely have some influence too (but I've never really pushed those values to extremes to see what they are capable of influencing).