Lots of these aftremarket mufflers drone. The previous owner of my car had installed a cheap Y to Y pipe system with dual mufflers and they were incredibly annoying at highway speeds. My solution was to replace the system with a true dual, and I bought used GT mufflers off craigslist.
If you have the option to replace the mufflers then you should. You could rip out your trunk liner and install dynamat under everything, that will help somewhat, but the real issue is improper tuning of the mufflers by the manufacturer.
2005 4.0 MT dual exhaust GT mufflers GT suspension and wheels