Take a look at the following diagram, which shows the main rendering chain:
Diving into this a bit: Layers - actually what CoGe refers to as ClipSynths and SyphonSources - are the mechanisms that render the image data (see the next section for details) - and the rendered image is passed to the Mixer.
All Layers and the Mixer are also Syphon servers - see Syphon section for details - so the rendered image at this point is also available to any apps that have Syphon support.
In the Mixer, images from Layers and/or Syphon sources may be used in transitions and/or compositing. The Main Output window always shows the image coming from Mixer.
The Preview window renders Syphon sources, as well as the Layers of CoGe. This is important, because if you are using any other application that is sending images to Syphon, these sources will be available in the Preview Selector list and you may view the incoming frames in the Preview window.