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I am running two 12" Rockford Fosgate Punch Z Subs with a Jensen XA2250 500w Amplifier. Since I am running Subs off of my amp I have the Crossover set to Low Pass Filter. It sounds great but recently I took my box out for a road trip and in putting everything back in, messed with the gain/low pass filter knobs. I set the gain pretty well and I moved the Low Pass Filter to a good setting but I am not sure what I should be running that at. The Low Pass Filter goes from 40Hz-240Hz... does anyone (someone a little more knowledgeable about sound and acoustics) know what I should set it to?

Depends on the sub and what kind of response you want. Pretty much any sub will handle that frequency range. I'd probably put it at 130 or so, but thats just me. You won't do any harm playing with it, crank some music and toy around until you find the setting you like the best.

around 100hz after that it gets into mid bass

For the best sound and most reliable performance etc not damaging subs I use a low pass at 100hz and a subsonic at around 20-25hz depending on the response of the particular car. The lower the resonant frequency of the car the lower the subsonic as a good rule of thumb. For instance my 2001 hyundai sonata has a res freq of 49 hz so i use 20hz subsonic. My 93 mx-3 has a res freq of 56hz so i use a 25hz subsonic. For those who have no clue what subsonic does it cuts out low frequencies that either the box is not tuned for and reduces overexcursion of the sub at low frequencies, etc a box tuned for 25hz with a 20hz note played for it will unload the sub. Unloading a sub is basically making the sub jump out of its basket, not a preety sight. I actually had a box tuned recently by a guy and gave him all the dims and specs and he tunned it wrong. It cost him a $550 dollar sub. The specs i gave him were for 56hz, he tuned it for 60hz by accident with a little 1 1/2" error on the port length. I tested it once @ 56 hz and it jumped literally past the voice coils extension and wrecked the sub jamming the coil on the pole piece.