All FlatRedBall shapes inherit from the PositionedObject class, so they inherit the X, Y, Z, and Position properties.
The Z value of shapes impacts their rendering, but not collision. In other words, shapes will render differently according to their Z value when rendering on a 3D camera, but they will collide as if their Z values are all the same.
Position relative to the Polygon
The Position of the Polygon is a bit of an abstract concept because it may or may not represent the center of a Polygon. In fact, it may not even lie inside of a Polygon depending on how the Points values are set.
If you use the CreateEquilateral or CreateRectangle functions, then the Position will represent the center of the Polygon. If you have constructed the Polygon yourself by setting the Polygon’s Points, then the Position value relative to points depends on the values you’ve assigned to Points.
Shape vs. non-Shape sorting
Shapes and non-Shapes which are on the same Layer (or which are all un-Layered) will not sort with each other. For more information see the ShapeManager.ShapeDrawingOrder page.