I had terrible resonance in my car (convertible), I had Magnaflow, very loud ones, changed to Flowmaster 50 series, a bit softer, but still a lot of resonance, they sounded great exterior, nice rumble, and I think the resonance was due to bad headers, and a stainlesss steel exhaust system.
I had no damping inside the car at all. Now the car is in pieces, I have a new TTI system (not stainless), and new TTI headers and Dynomax mufflers waiting. I'm also changing the engine to a 6.1 Hemi so it will be a completely new setup, I will use Dynamat or similar when I put it together again. Resonance is hard to get rid of, most of the time it comes from the mufflers (acoustic), but it can also be mechanic, check so the exhaust system is haning free and not touching the body at any point, and the hangers have good rubber. Can be as little as the exhaust tips touches the rear valance, that can make the whole car resonate.