From that diagram it looks to me like the Bass amp is driven from the speaker outputs right before the Front/Rear Fader, so that the bass stays on even though you fade from front to back.
If you can find that Bass amp maybe it has a trim pot on it.
Or just turn up the trim on your JL and see if you can get your ideal balance where the bass speaks and the dash ones start to sound like crap at the same time.
Is it this?
