I also have the nav, so I didn't want to upgrade the head unit. To get more bass, I added an Alpine sub and a pioneer 10" subwoofer in a down firing enclosure. I choose the down firing enclosure so that I can still use the trunk without setting anything on the woofer. This has worked great for me. More bass than I need. Since the amp I used had speaker level inputs, I didn't need to add a line converter. I just tapped into the wires going to the stock subs in the spare tire. I put the amp on the shelf behind the driver's seat. If I want to, I can take the sub completely out in 2 mins and have full access to the trunk. It was ~$400 for amp, sub, wire kit and remote knob.
PIC LINK
LINK to Sub
Link to Amp
LINK to Power Kit
Link to knob