Within SPAN I remember this being an issue, and could not get it to do multi-channel analysis properly, but it will do left/right channel analysis without much fuss. The easiest way to do this is to use two mono tracks, one panned left, the other right, and feed a buss from them. Put SPAN on that buss and set two of the inputs to the left and right channels respectively.
*If* you own Neutron, I would actually default to that since it has more features and is simpler to set up and swap inputs with.