Well I managed to get a hold of this today for close to the original price, so once I've given it a read, I'll try and help some more.
What I can clarify, which may help, is the order of the albums in the story's timeline.
The Afterman: Ascension and Descenion - Album Released 2012/2013 and covers the character of Sirius Amory and the origins of the Amory Wars saga.
Year of the Black Rainbow - Album Released 2010 and acts as the first part of the Amory Wars saga.
Second Stage Turbine Blade - Album Released 2002 and links to the second part of the Amory Wars saga, though their first album.
In Keeping Secrets of Silent Earth: 3 - Album Released 2003 and links to the third part of the Amory Wars saga.
Good Apollo, I'm Burning Star IV, Volume One: From Fear Through the Eyes of Madness - Album Released 2005 and covers the character of The Writer, pretty much t he fourth part of the saga.
Good Apollo, I'm Burning Star IV, Volume Two: No World for Tomorrow - Album Released 2007, no graphic novel has been released but is a sequel and continuation of the fourth part of the saga.
I have read some of the first issues, that my friend owns but I still don't have my head fully wrapped around the story just yet. The albums aren't a must if you have the comics but they do compliment each other very well. You understand the narrative of the songs more, and vice versa.