I'm one of the writers: thank you for the kind words.
The trick to follow the Seeds Of Deception comics is browsing The Gallery
On the left side of the screen, there is a list of folders: each of them hosts a chapter of the series.
They are in a relatively proper order, at least when it comes to the main chapters: 1 Omega Supreme, 2 Trannis...and so on up to 9 Starscream.
What you need to remember is that their stories take place in parallel, not in sequence: each chapter tells events of the Golden Age from a different perspective, focusing on different years and/or locations. There are many internal links which build a larger tapestry: the notes to each page (you can see them by scrolling down the page) will provide a detailed guide.
(The pages of our comic are all gathered under one single DA account: there is also a road map
There are some additional folders, providing extra chapters, like "Magnificence Saga" and "Short Stories" which are written to connect The War Within to other of Simon Furman's works.
There are tales from the Nova Prime Age as well (before the Golden Age): "The Evil That Mechs Do", "Constant Moon".
"Dark Side Of Sentinel" is a SoD/Dark of the Moon/Revenge Of The Fallen crossover.
The last folder is "Wrath Of The Ages", which reached page 12 but more aer being colored right now!
(We need more skilled color artists, btw. HINT HINT HINT!)
To answer your question, yes, we are following the story summaries seen on TWF2005: see the notes to page 1 for more details.