I originally wanted to map this in chronological order, but there was very little intersection between the series like that.  And when the line fizzled out, I decided the best approach was to bind it by series.

Captain Midnight volume one
Project Black Sky Secret Files TPB (except for FCBD story)
Dark Horse Presents #18-20 (Captain Midnight #0)
FCBD 2013: Star Wars/Avatar/Captain Midnight – middle story only
Captain Midnight #1-7
Skyman #1-4
Captain Midnight #8-11
Two Past Midnight #1-5

Captain Midnight volume two
Free Comic Book Day 2014:  Project Black Sky
Captain Midnight #12-16
Skyman one-shot
Captain Midnight #17-24

The FCBD story is reprinted in the Secret Files TPB, and that’s what I used here.

Ghost
Dark Horse Presents #13-15 (Ghost #0)
Ghost mini series #1-4
Ghost #1-12

X
Dark Horse Presents #19-21 (X #0)
X #1-24

Brain Boy & The Occultist
The Occultist one-shot
The Occultist #1-3
Dark Horse Presents #11-13 (Occultist story, not reprinted in #0 issue)
The Occultist #1-5
Dark Horse Presents #23-25 (Brain Boy #0)
Brain Boy #1-3
Free Comic Book Day 2014:  Project Black Sky
Brain Boy:  The Men from GESTALT #1-4
Dark Horse Presents #7/200 (Ape-X story)

I know, the title is backwards of the contents, but it flows better.  The 2014 FCBD story appears again, this time binding the original issue.

Quis Nisi Nos
Dark Horse Presents #24-26 (Blackout story, no #0 issue)
Blackout #1-4
Barb Wire #1-8
Blackout #1-4 (King Tiger backups)
King Tiger #1-4

This last book is just a catch-all of the last few minis that didn’t really fit anywhere else.  Barb Wire and King Tiger didn’t even carry the PBS trade dress.  I considered putting all of the short series together (including Brain Boy and the Occultist), but the book was just slightly too big for my preferences.