Which amp do you have, mine is the MRD-M301, running a JL 10W3 at 2 ohms. My amp settings are input switch to 4 volt, input 0, gain 0, bass boost off, Low pass set at 80/24( used the amps lowpass instead of headunit sounded better that way). Subsonic filter off(sealed box for me), Eq off, and make sure you save your settings with the last menu item (memo). YOu can name amp 1 with preset of 1 or 2.
My headunit crossover for front and reat are at 100/12, and the subwoofer I have set to 80 flat, this way it won't interfere with the amp low pass. Now to get the best benefit out of this amp and this headunit I had to make it where my normal listening level on the headunit is 23-26. The front and rear preouts seem to be much stronger than the subout(been told that the subout only produces the 4v with the hu sub volume set to 15.) With these settings I get great out put and have my hu sub volume set to 8 or 9. I can run the headunit to 35 with no clipping or distortion, but normally max for me seems to be 30.
You will have to try and see how these setting work for you and compensate.
Bill3508