Unfortunately, Brawl doesn't automatically detect the colors. If you want the custom textures/characters' colors to be consistent with the team colors, you would have to manually put the character over the color/texture slot you want.
Well yeah, of course. But something has to tell it to select one slot over another.
Edit:
If you were asking if it is possible to change the slots it chooses for each color; its probably possible via codes, although there are no codes I know of that can do this.
Alright, so that puts us back where we started, which is basically the same exact thing I said before. xD