Since none else answered. I'm no JL guru, but I have JL amps myself. Mine all get a direct signal from the RCA's off the deck, so I don't know how using the preamp outputs affect anything.
Did you run sufficient power and ground cables to the new amp?
The settings should be the same at the the other amp, except maybe the gains.
Also speaker location and type of space behind the speaker can affect sound quality.
J