I tried putting my scenes on note cards first. Let me tell you, drop those suckers once and the entire system buckles. Especially when you have an intricate intermixing of “present day” plot, “childhood flashback” plot, “a few weeks before present day” plot, and “stuff my character did in real time but forgot because using his magic gives him amnesia” plot.
Thus, I became a recent convert to the Scene List discipline. Four pages. Not an impossible puzzle to reassemble if dropped. Unlike this catastrophe.
I learned about scene lists from this article by Monica M. Clark, in which she illustrates the usefulness of creating a scene list to keep yourself organized. Before I read this article, a fellow writer told me about an interesting method used by J.K. Rowling in plotting The Order of the Phoenix, which included a column for each subplot and which chapters added to that subplot. For example, under the “Cho/ Ginny” subplot, the interesting development “Harry finds Ginny snogging his roommate behind tapestry” would be included.
Personally I found the subplot tracker the most useful in this exercise. I’ve had difficulty remembering what stage the subplots are at in the various timelines and what my characters know about them. (Unless it’s Amnesia Guy, in which case he probably knows nothing. Figures).