You are mixing the 2 things up, banana.
The amount of energy in a closed system with an atomic bomb is constant.
Usually when looking at atomic bombs you don't look at the closed system, because that is meaningless. You usually want to know how much energy was generated by the annihilation of some mass.
In the closed system, mass, energy and c are all constant.
In the open system there is an amount mass that is annihilated which equals x, and there will be an amount of energy generated by this amount mass which equals y. If you want to calculate y, you use the formula:
y = x * c^2.
The amount of y depends on the amount of x, right?