I was very impressed by "Nocturnal", especially given you were writing it as you were podcasting it.
To me, there were two distinct stories going on:
1) Rex and Bryan both discovering their heritage and choosing two distinct destinies that collided on the boat.
2) The "origin", such as it was, of the Nocturnals/Saviors/Kings. That includes the Groom's Walk and Marie, and mostly focused on Aggie.
As far as breaking the story up, I would recommend the following. Strip down the first novel to focus as much as possible on Bryan and Rex. Save the part with Aggie and the reveal of Marie until the second or even the third novel. I know that flies against your normal pattern of explaining the monsters, but in the case of a story that lends itself to a trilogy you can afford to leave the readers waiting. You can still point out the chromosomal abnormality, but keep its true nature quiet until the readers can truly appreciate just how horrific the source of the Children is (something that would come after they are truly immersed in the Nocturnal world).
I would imagine the sequence would go like this:
Book 1 follows Bryan and Rex as they discover their true natures. We introduce the monsters, do the whole crime syndicate story, but we don't get too deep into exactly -where- the monsters come from. It ends exactly where the podcast ended, with Rex dead and Bryan embraces his destiny as the Savior. We get a glimpse of the Nocturnal underworld, but we don't see Marie or the undreground ship.
Book 2 continues the story as you've envisioned it, but now we can add in Aggie's story and show how Bryan and Rex were rescued from the underworld as babies. I would even suggest not showing Marie yet...just have Hillary give Aggie the baby and show the Groom's walk (but not the conception scene) to give Aggie some motivation.
Book 3 finishes the story, but here we finally see Marie and how new Nocturnals/Kings/Saviors are conceived and born. The shock factor of Marie would go great with whatever finale you have in store.
Again, you've got a great story here. It's definitely epic enough to warrant a trilogy of books or more. As much as it pains me to admit it, you might even want to poke the brain of Hutchins and find out other ways to spread it out over three books, since he did a good job doing that with 7th Son.
Thanks for the entertainment, and I look forward to meeting you in Dallas next month :)