Make sure your subs are wired up right and not out of phase as said before. Use this link to verfiy your wiring.
JL Audio
(this is if you have the JL audio W3 version 1 or Version 2 only which have dual voice coils.)
JL Audio
(this is for the single voice coil W3v3 only.)
you can tell if you have them wired up in phase, by taking a 9-volt battery and putting the + speaker wire on the + of the battery, and the - Speaker wire on the - of the battery. Both speakers should pop out towards you. If one moves one direction and one moves another, they are out of phase. If both move in, when you have the positive and negative matched up with what's on the battery, then the are reversed phase (also out of phase).
Now read how to set your gains on your amp.
JL Audio
Or in dummy terms, just turn the gains on the amp about 3/4th the way up, bass boost should be no more than 1/4 to 2/4 the way up. Make sure the RCA output from the deck is connected to the non-fader (subwoofer) output. Also make sure the crossover switch on the amp is set to Low Pass. If it lets you adjust the frequency range for low pass, set it to play about 80 Hz and down. Your amp manual should tell you how to do this.
Hope this helps, if not, you will just be better off taking it to a shop and letting them do it for you.
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Also make sure your subs are wired in the right ohm load for your amp. Wire it too low, and the amp will blow or not perform right. That's about all I can say.