No it's not possible with the current theming system. I am confused why you would want it. The top waveform is the left and the bottom is right. Simple. Anyway...
It may be possible with version 3 as you can now add images as backgrounds, but the waveforms would still be one colour. Red and blue backgrounds would definitely give you the differentiation you are looking for.
version 3 alpha is available here and in the pre-release section of the forum:
http://forum.cockos.com/showthread.php?t=22836