I am not 100% sure about what you are asking here, but it does indeed matter which color cable is in which slot. If you were to put the 8 pin PSU cable in upside down it wouldn't work, for instance. At best it wouldn't turn on and at worst it would actually damage hardware.
If you had a whole slew of, say, black wires and you use tweezers and remove them from the connector and then re-insert them in some different order than they were originally in, that shouldn't matter. As long as each color is in the right place it should work.
That being said, I wouldn't go around re-arranging these wires for the fun of it. The PSU could theoretically be wired in such a way that it does matter and that could turn out to be a bad thing. This sort of problem should be a really remote possibility, though.