I dont have an 08+ but I do have a 2006 with the factory Bose set up and Navi. I used a PAC interface to add a amplifier to the factory head unit, I hooked up an older 12" Pioneer sub with a Alpine amp (had the stuff sitting in my garage), I also added the Nucleus ipod integration (lets you control the ipod through the factory navi unit). The system sounds amazing, I have a friend who also has an 06 H2 that spent alot of $$ (around 6 grand) having a shop do a full out custom install on his rig and while it sounds good, its not much better than mine sounds (not 6 grand better). Everyone who has heard mine is really amazed at how good it sounds. I did the exact same thing in my Z06 and the result is the same...... 10" Rockford sub in a custom made enclosure (similar to the stealth box) with a Rockford amp, PAC interface and Peripheral ipod2car.
Add just the sub first and see if it satisfies your needs...... if not then you can start adding on. PAC makes all of the neccessary interfaces to add amp(s) to your factory head unit. Good Luck