Its my understanding if you flip a double card with CB, that you get to chose one of the individual spells. I was looking it up the other day, but i might have misread
There is no choice involved, the effect will simply use both numbers. In the case of Counterbalance, it asks the question "Does the CMC of the revealed card equal the CMC of the spell?" If you flip Boom//Bust, the CMC of the revealed card will be 2 and 6, so if the CMC of the spell that triggered it is 2 or 6, the answer will be "yes," and the spell will be countered. If the CMC of the spell is 2, you cannot reveal Boom//Bust then choose to use the 6 and not counter the spell.