Some screenwriting software allegedly, and I emphasize the word "allegedly," walks you through the process of constructing scene structure for a feature film script--holy Ishtar!
By far the most useful tools I've found, other than my Macbook pro, and Final Draft screenwriting software, are low-tech products that have been around since before there was any such thing as movies, let alone screenwriting software. It's the standard bulletin board, push pins and index cards.
This is not news to readers of Syd Fields and other screenwriting instructors. But for myself, it was a revelation after years of resisting the bulletin board. Turns out, it's a flexible, inexpensive way to plot out your entire script, and its most obvious advantage is that you can take in the entire story at a glance.
If you establish a set number of cards that you will post to make up a script--the standard being 40, at least for me--you can immediately tell what part of your story is missing and needs to be filled in.
Save yourself a lot of headaches by using these tools and you'll be amazed by how much easier it is to keep your story on track.
