I have some of the Boom/resonance issues in my coupe but it has gotten better with time. The Magnaflow was kinda "raspy" when first installed but it has mellowed with time (approx 4-5K miles). The hatch back structure of the coupe is part of the resonance problem. An extra resonator will help some but you may want to try some dyna-mat or similar acoustic treatment under the cargo area carpet. That open area acts as a acoustic "bass trap" and amplifies that particular frequency. This is a common problem with hatchback coupes in general. There is also some leeway in how far the back half of the Magnaflow system slides onto the middle pipe. I pushed mine back as far as possible. This makes the rubber "donuts" tighter, gets the hot gas and noise out from under the car and away from the bumper fascia (see pix in my gallery) On my car the tips protrude from the opening by a little over an inch. There is a downside; you can burn your ankles on the hot pipes when getting into the hatch. I keep a big towel back there and drape it over the rear when loading/unloading to prevent burning my ankles or scratching up the paint.
Slim