I have an Electra-Glide Classic and knocked out both plugs on the left pipe. On the right pile, I knocked out the back plug and drilled a half-inch hole in the front plug. I did this to help equalize the exhaust pressure throughout the system. The right pipe does most of the work as it.
Doing this did relieve some of the exhaust back pressure and helped the engine to breath better. I'm still looking at a Stage I and Scream'n Eagle pipes. Knocking out the plugs is a good start though.