First, download iw_sky.iwd in attachment (its modded sky files) and place it in any mod folder in cod,
then record what you want with fraps (with blue sky) and then open your vid.
in After Effects (you can also use Sony Vegas, but i will use AE).

(I will change sky on this screenshot for example)




In AE select Effects & Presets -> Keying -> Keylight 1.2 (in SV its called "Color Key" or "Chroma Key") and in "Screen Colour" select blue color.



Then, in AE / SV create new layer and put your sky video / image or make it with any Clouds Generation plugin
(i use GenArts Sapphire plugins for this, you can also create clouds in Photoshop
(http://www.youtube.com/watch?v=fW0y_ePz7ic i made this clouds with CS3).



And then Export (you can add. some effects before export it) it to .avi (uncompressed) or screenshots files
if you will edit it with any another programs.



Enjoy your new sky in cod.



Final result of this tutorial.