Bingo, no, the Alpine amp only powers the JL sub. I kept everything else factory. After the install, I am incredibly happy with the sound. The JBL components are fine with the exception of the factory sub which is a joke.
Essentially, I have disconnected the factory sub from the factory amp and converted the amplified signal back down to low level inputs and then fed that to my Alpine amp. Here are a few shots of the completed system. The only other thing I think I may install is an iPhone integration adapter to interface with the factory system.
Stock Navigation JBL system
Pro Wedge 10W6v2 in the rear:
Alpine monoblock amp under the front seat, seat all the way forward to show install:
Sub level control mounted in change basket:
8 gauge power wire and fuse block: