The first and most important thing to remember about the Polygon Tool in the GEM editor is that it can cause serious lag if you use too many very small polygons. Lag both to you when creating and lag for the player when playing your map.
The short video below shows you where to find the tool and how I use it. This video like all my videos uses closed captioning so enable this if there is no text shown.

The below video shows you why I use it. I find it best used in situations where you wish to place an entity that has a vertical wall, e.g. Cliff walls as shown or Town walls, and space may be of a premium. There is no captions in this video as it wasnt needed.