Think of the game structure as a skeleton that holds the body together. Without it, your game will be a jumbled up, confusing mess - kind of like an amoeba. You can start off by creating a text-based, hierarchical map of the game. Just write out all the steps, what characters and what interactions occur. Many people have a hard time seeing something like the game structure listing and translating it to the way the game will work.
Architectural blueprints can help.
They are diagrams showing how elements of the game are grouped and how they link or relate to one another. Defining the navigation system for the game solves these problems.