Keeping Track of a Complex Story

As I've written In Chaos Forged, the complexity of the story grows, and as the complexity deepens, so will the length of the story and the Hammer of Fire series overall.  How do I keep track of the details in an increasingly complex story?  I'll offer a few things I've done for In Chaos Forged and other stories I've written.

• Keep Side Notes - As I introduce new concepts, people, and groups into the world, I'm usually not able to explain all the details of those things right away, especially when I write about factions. 
• For people, I'll keep notes on their personality, their abilities, and how they interact with other characters.  I haven't written large character sheets for them, though; I'm the kind of writer that discovers a character as I go along.
• For concepts and factions, I'll create a document detailing the what, the why, and the hows of the ideas.  What is the concept?  What do they do?  Why did they create the faction?  How does the idea work?
•  I've kept most of my major notes on computer documents, but I also have a notebook app on my smart phone where I can keep notes on the go.  I've also used a hard notebook to keep many notes in.  Small notebooks that can fit in your pocket or handbag are very useful as well.
• Use Bookmarks - In a word processor, there should be an option to insert bookmarks throughout the manuscript.  I use Libreoffice and Openoffice.  Go to Insert>Bookmark... and you can type the name of the bookmark and press okay.  It will insert the bookmark wherever you have clicked the cursor in the manuscript.  You can press F5 and it will bring up a document navigation screen, and there will be an expand option to look at and access your bookmarks by double-clicking.  I've used this tool to mark important events, settings, and ideas in the story that I may need to refer back to later for consistency.
• Think about your ideas often - I've found that thinking about my story ideas often while not writing or editing helps things click together and I can note them down later.  My life is a little crazy, but I still find time to think about my stories.  Your brain is like a computer, and if you ponder an idea enough, it's likely to fit together and make your story work, no matter how complex your story is getting.

Hope these tips help the writer out there who is also digging through an epic story!