To add on to what A/V1 stated, the speaker wires provided off the bypass harness will now go directly to the speakers in the truck and bypass the JBL amp so you can either use the headunits speaker output and use its internal amp or you can extent the speaker wires from the harness to where ever you want to install an aftermarket amp for your highs and get real power to your speakers, which from your stated equipment, is what you are gonna do. If the JL is small enough mount it under the drivers seat. You will only have to extend about 6 feet of speaker wire tops.
My Phoenix Gold Ti 5 channel under my drivers seat putting out 150W rms to each of my 4 speakers and 950W rms to my 2-12" subs. Fits perfect and takes up no useable space.