FlexColor is not quite as advanced I am afraid.
It was written primarily for tethered captures. ie. Shoot Custom White, Apply, Shoot actual Image, and not much flexibility otherwise.
However, if you have captured some images to CF card, or an Image Bank, if you import the CW shot, apply it and then import further captures, they should also have the CW applied.
I am going from memory and haven't tried in a while, but have a go and let me know if it doesn't do the trick.