you have to discard the rainbow with Rayquaza, there is no choice.
For example: Ray' 1 Fire energy and 1 rainbow attached. If you decide to discard lightning energy, you discard only the rainbow. If you decide to discard fire energy, you must discard both. This is because rainbow provides all types at once, but only one unit of energy.
Also, multi works the same way, unless there is another special energy attached of course.