Well it sounds like I may have been doing things the long way. I don't want to labour the point to much, but does that mean in an app like deepsky stacker or registax I could simply load all the subs that were taken (eg 50 red, 50 green, 200 blue, no lum) as well as any flats, bias etc, and just run it in one go?
To think, I have been processing each channel at a time, then manually stacking the result.
I may have just increased my productivity here by 300%.