When I initially installed the Cobras, I did so without any baffles. It was too loud, (and I'm saying that coming from a Harley) and the other thing was not much back compression.
Putting two baffles back in on the shorter two pipes lessen the drone and put the back compression back to "normal". The longer of the 3 Cobra pipes sticks out beyond the saddlebags. Therefore the sound isn't resonating under the saddlebags.