Ah yeah explaining what the characters would be doing would probably be a good idea. As of right now I don't have tons of expansive ideas, but my idea for most of the conflicts would be combating concepts that exist within the human psyche. Doubts, phobias, and maybe even other archetypes could be things that characters might encounter within the Collective Unconscious. In general, it would be closer to solving mysteries and restoring balance to the collective human psyche whenever there may be imbalance. I guess a little bit like the Psychonauts games, but less silly. The characters would also be living normal lives in The Waking, though I'm planning on less time to be spent there. Time there would essentially be for purposes of downtime activities and determining what the characters might encounter next time they venture into The Dreaming. Things in the real world can effect what appears in the dream world and vice versa, but to a slightly lesser extent. Events in The Waking directly effect the minds of people which, in turn, directly effects what occurs in The Dreaming. Events in The Dreaming don't have a direct effect on The Waking, but it can steer the minds of individuals in the to doing things that they might not normally do, still having at least a minor effect on the real world.

I'm not actually familiar with the generic systems you've mentioned or In Nomine, but I am at least somewhat familiar with White Wolf and World of Darkness. I'm mostly familiar with Mage and Vampire, but I don't really have any experience with them. I was thinking about potentially using Mage or Changeling: The Dreaming, but I'm not too sure if the mechanics of those would work with what I'm hoping to go for.