Writing a complex story can be confusing. It is hard to keep track of characters and events if they diverge from each other. It is important to have a system so you can keep track of everything that is swirling around in your head. A complex story should be challenging for the reader as well as the writer. The more story arcs there are, the more complex and more difficult it will be to write your story.
Write an outline for yourself. This can be done in many different ways. It can be a timeline or a mind map. It is also good to write down all your characters and write at least three sentences about the character. This will help you fill out your ideas and make the events and characters in your story more concrete. It is a good idea to write down what the relationships are between each character and how they develop as time goes on.
Talk with someone about your story. Verbally explaining and expanding on your ideas will help you gain a further understanding of what you want your story to be about. If you have an editor, he is an ideal audience to have this talk with. If you do not have an editor, talk about your plot with anyone who will give you sincere, constructive feedback.
Plot your story. According to www.spacejock.com.au this means to write out your whole story within two or three pages. This should be a summary that encompasses the whole plot. The reason for this is because it is much easier to revise two or three pages than hundreds. Of course, this may not work for everyone. Many writers simply plan out scenes as they write. This can become confusing, though, and it is important to keep a storyboard at times to keep track of the divergent plot arcs.
Write your story. It is important to keep notes on everything that happens in your story. Don't become chained to your outline. It is only that--an outline--and if inspiration hits and you find that something can be changed to make the story better, go for it. Use every bit of inspiration to build your plot--just make sure to take notes about it. When you become confused within your various plot arcs, your notes will be very useful.