My wife's 2011 Genesis Coupe has the stock premium sound system with NAV but she didn't like the factory sub. As a result, I put a dual 2 ohm True Bass 8 in there with a 500 watt Lunar L1500 @ 1 ohm. I have the amp and PAC SOEM-T turned all the way down and it blends perfectly with the stock setup that has a factory center. I think she set her mids and highs a little on the bright side for me, but that's how she likes to listen to her setup, so, if she's happy, I'm happy.
My only complaint is that I built a test box out of particle board shelving, and she won't let me rebuild it with Birch. Oh well...