To fight against the bad seeing condtion and atomsphere dispersion (From my location mars only reachs 33 degrees above horizon) I was using color filters to get different channels.
My setup is C9.25 + 3X barlow + homemade filter changer + Astronomik filters(Thanks Mr.Sean Walker

+ ToUcam
Normally I only use Red and Blue filters. The green channel is the average of Red and Blue(according to the S&T article). I found the seeing is always more stable for blue light than the red light (can anybody explane this?) But mars won't give enough blue light to get a good signal noise ratio.
I align all the frames in Registax 2.0 but stack and process them with registax 1.1(which I feel is better for some reason). The finally RGB assembling and adjustment was done in Photoshop.
Attached are the typical selected Red and Blue channel raw frames.
clear skies,
GY
http://planets.lamost.org/