The software is called "Scrivener." While a basic word processor has all the necessary features for composing a story, Scrivener allows me to create separate chapters, scenes, and so on, and then merge them or rearrange them as the novel begins to take shape. I can also jot notes about what I want to do with a particular chapter--that portion of the story arc--and a summary of the scene so I can easily find a particular portion of the story when looking back through it.
This manuscript is now in the hands of my editor. Of course, I'm still going through it, too, refining word choices, making corrections, etc. Even last night, as I was doing something else, I suddenly realized that one clue I'd given early on in the story was never resolved. I'll go back and fix that today.
There's always something else to do to a manuscript. It's never really "done," although at some point an author has to call it quits and put the book out there if he or she wants others to read it. I no longer want to keep unread manuscripts in my drawer -- that's not my goal. I want to share stories with you in the hope that they may make you smile, cry, laugh, frown, and hope the good guys win in the end. You're the reason I write.