Very often, writers will put every scene and idea on a separate note card, and then shuffle the cards around a cork board in order to find the most effective order. Naturally, there’s a lot more too it than that, but you get the idea. This technique has been around a long time, and is still widely used today. For those that like modern parlance, consider it mind-mapping for screenwriters.
There’s a LOT of mind-mapping apps in the App Store, but so far, only Index Card offers the ability to export your organized cards as an RTF for importing into Final Draft (the de facto standard for desktop screenwriting software). This feature alone puts it WAY ahead of the pack.