There are several windows in the top level editor that control the order and layering of your scenes.
Scenes Window
This window shows all of the scenes that you have in the document. Scenes are the basis for all of the graphics in the document; the top level is only concerned with the order and position of scenes and not directly with any graphics itself.
Double click a scene to bring up the editor associated with it.
Layers Window
This window shows all of the layers in the document. A layer is a set of views and modes, and by using multiple layers you can combine 2D and 3D graphics together.
The topmost layer in the list is drawn first (the background), and then each subsequent layer is drawn over the top of the last.
Use the checkboxes to show/hide layers from being drawn in the editor.