Excepting the confusion between the relationship of mass and energy which you cleared up, that was a totally legit question: Energy gravitates, so we do in fact need to know where all (non-gravitational) energy - including contributions we label 'potential' - is located if we want to determine the metric.
The answer to the question of 'where' is the underlying (non-gravitational) physical field (and in particular the electromagnetic field, which is long-range, whereas the nuclear fields normally get folded into mass terms). The case of gravitational potential energy is a bit more subtle: It's excluded from the stress-energy-momentum source term of the Einstein equations, and there's no expression for a gravitational stress tensor (though there are pseudo-tensorial approaches).
The answer to the question of 'where' is the underlying (non-gravitational) physical field (and in particular the electromagnetic field, which is long-range, whereas the nuclear fields normally get folded into mass terms). The case of gravitational potential energy is a bit more subtle: It's excluded from the stress-energy-momentum source term of the Einstein equations, and there's no expression for a gravitational stress tensor (though there are pseudo-tensorial approaches).