What does Jekyll mean when he says that in the "agonizing womb of consciousness, these polar twins should be continuously struggling"?

Dr. Jekyll means that we are not supposed to be able to separate our evilness and our goodness from one another.  Part of the fundamental struggle of being human is that these twin halves must wrestle with one another for control over our individual psyches.  Thus, this struggle feels agonizing because it is never really finished; we are constantly tempted by the darker sides of our natures, and we must work to strengthen the light so that it can prevail.  His reference to this state of consciousness as a "womb" could be seen as quite accurate since our selves are never really done developing; we are, in a sense, constantly gestating and becoming, never quite finished.  When he utters this sentiment, it is because he has realized the egregious mistake he made when he attempted to separate out his evil side so that he would no longer have to endure this struggle.  He realizes that the struggle is, itself, a vitally important part of being a human being.