Flow charts and diagrams are a very powerful tool that every designer has to learn to utilize. They can be used for anything from explaining the ins and outs of your game economy and gameplay mechanics, to portraying technology and skill trees.
Unless your game is trivially simple (or a near-direct copy of something existing), you'll need to create a flowchart of sorts to explain where various options and features fit in and how they are connected. Even a simple game of Rock-Paper-Scissors could have its flow represented by a chart:
In the preceding example, we can ...