i have also posted about trying to use the stock head unit and adding my amp and sub and nobody on this fourm seems to have anything good to say other than the stock sub is a POS or you need to change the system or something else that states the obvious.
today i spent a few hours and actually wired in my sub to the factory HU. all i needed was an amp. my sub+box. and a wire kit. (inline fuse 8 gage wire and all that fun stuff) and some tools
from what i have found researching is that the stock sub (with bose) is amped at 100w so i dont know how much more you can push it.
once i wired in my 12" sub i started to tune it and it had a weird sound to it. with all my messing around i decided to remove the factory 9" sub from its home (it wasn't wired) and all the weird noises went away. i think the displacement of air in the trunk from my 12" was making the 9" factory sub kinda hit just because of the movement of air and it made the car sound like shit. once i removed the 9" the car sound had the nice aftermarket stero sound.
BEST thing i did other than add the 12" was taking out the factory sub.