I would highly recommend having someone that knows what they are doing to tune the amp. You can follow the gain setting tutorial on JL's website, but if you have the gain too high and play your music too loud, you risk damaging your amp and/or subwoofer.
Here's a few info on some of the settings.
Infrasonic Filter (also known as subsonic filter): Some amps have an on/off switch like the JL, others have a certain frequency. If you are going with an infinite baffle or sealed setup, I'd leave it off. If you have a ported setup, you set it according to the tuning frequency of the enclosure (usually a few frequencies below is ok). I had a Kicker ZX and I believe the SSF (subsonic frequency) was defaulted to 25 HZ. Basically, any frequencies beyond that frequency are cut, not completely, but enough to where it where it helps prevent damaging the subwoofer. If your box is tuned to say 35 Hz and you play a 16 Hz note (rare, but some tracks, like bass tracks will have that), the sub will bottom out. Think of a subwoofer as the car's suspension. What happens if you hit a big dip and you're lowered? The car can bottom out. If it does that constantly, your suspension is damaged, and in the case of a subwoofer, it would need a recone.
The Boost, is for the bass boost. You adjust this BEFORE setting the gains, but I always recommend leaving it at 0 or off. Yes you get more bass with it on, but all it does is boost a certain frequency, and that depends on the amp. Image a straight line and on the line the frequency range is from 0 - 120 Hz. If 45 Hz gets boosted, it would be like dragging that 45 Hz point on the line upward. The more you turn it up, the more it boosts the frequency, and other frequencies get boosted as well, like a bell curve. The problem with this is, that it's only boosting a few frequencies and not the entire spectrum, so if you want more output, turn up the gain instead, or if it is at its safest level and you have enough power going to it, redesign the enclosure or get a new sub.
The LPF or low pass filter is the frequency you set where the subwoofer will not play above those frequencies. What you want to do is match this with the HPF, or high pass filter that the midbass speakers will be playing.
The input dial, or gain, allows you to adjust the amount of signal an amplifier receives. It is NOT volume ****. Although the loudness of the sub increases and decreases by adjusting, what you are really adjusting is the sensitivity or signal of the amplifier. Turning the gain down results in less wattage, turning it up results in more wattage. If you want to adjust volume, do it from the head unit.
Hope this info helps, and hopefully I didn't make it too confusing.
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