For my 06 X, without a factory sub, I found a used center console from a Rubicon that had the stock amp and speaker. Replaced the torn speaker with a new Kicker, and had a "Car Toys" shop wire it up to my factory 6 disc head unit/player. Nothing major, the parts were cheap, install cost was low (sorry don't recall the amount), and it Sounds great (for me).
Inside the console I have the factory CD holder storage tray. For me, the limited storage there prevents keeping a lot of unusable/lost crap, which is a good thing. I don't worry about theft, both the console lid and glove box lock. If somebody wants to get in that badly, have at it, I don't leave valuable stuff in there when I'm not in the jeep.
Theft of the sub components and head unit ? Possible, but not likely, who really wants to waste the time on stock stuff?
Ray