What visual design are you trying to achieve?
Can you create a mock-up of your design in photoshop and post it here?
If you would like to have transparency in certain areas of a static overlay, then render your overlaying image as .png with alpha transparency maybe.
On the other hand, you can add several Chroma Key filters to the same source. If the different areas of your screen have different and specific colors you can key out these areas easily.
I'm still not sure what you're aiming at. You example is easy to understand, but I think if you would post a more specific image, we may be able to help you more thorough.