as far as the software you're writing, the actual colors Red, Green, and Blue can be on any channel.
if i program the ssc to start on channel 1, then 1=red, 2=green, 3=blue
if i program the ssc to start on channel 2, then 2=red, 3=green, 4=blue
as long as I (the user) setup my equipment correctly with the config utility the color order is corrected by the SSC.