Hi. I had a JBL system that I removed 4 years ago. It didn't sound that great anyway. I had to run a wire harness from the amp location to the stereo to upgrade because that's where the JBL system speaker wires run to.
However, if you want a small sub, you could hook to an aftermarket head unit and hide it behind the interior quarter panel from a JBL runner... that would be slick. I finally switched (last week) my quarter panel to a non JBL version so I would have the storage compartment.
If I remember correctly I spent about $100 in adapters for the steering wheel controls,antenna and the harness from the rear when I did my upgrade.
Hope this helps a little!