I'm pretty sure he's talking about the struggles all of us share in a spiritual sense. It's as if he wants both sides, and feels divided by fighting one or the other, so to stay centerd he chooses to "Breathe in Union." whith both good and not so good. It's pretty cool that I was able to find some clues in these lyrics to discover that the "benevolent son" is actually Jesus, and to hear Maynard revearing him makes me like Tool that much more.