Power pyramid subs smoking i think the jl 1000/1 is tuned wrong..

Your sub is a 4ohm woofer, running it in bridged mode + on right connection - on left connect as market on sub will give the best output. Your sub is rated at 75w to 300w and in this configuration will be getting just over 100w which about all the amp can provide with your sub/amp combo.
I don't know where they get the 1000w rating from either? the maximum the amp can possibly provide is 150w if running a 2ohm woofer in bridged mode.

ok if u have a radio with sub controll make sure its on an make sure that you have the gain bassboost turned up an if it has a crossover switch make that its on

your aux cords could be craked or cut somwhere

you dont want to connect both of those amplifiers together. You could run them separately to separate subs or the jl to your sub and your alpine to your front speakers. But you dont ever want to mix and match amps to the same sub. Even if you had 2 jl500/1's you wouldnt want to just hook them up together. Because they both have to be putting out the exact same amount of power. Which no 2 amps are ever exactly the same. Some companies make bridges to properly connect 2 exact amps together. I Hooked up 2 JL 1000/1's to each voice coil on a 13.5 W7 and i smoked the sub. So i definitely dont reccommend doing it unless the amps are conneccted to separate things.

If the sub is new, they need to be broken in.

All sub woofers need a break in period of about 5 to 6 hours at medium volume.
The reason is because the glue needs to be cured. This is done by the heat from working.

If you are giving it too much volume too soon, you are burning the glue.

Back off the subs and only play them at medium volume for about a week.

its not the amps my dude ur ohm loading is wrong if u have a 4 ohm stabled amp n ur speakers r 2 ohms naw thats not gonna fly caus it cant put out what ur asking 4 so u need 2 reload ur subs try this link http://www.bcae1.com/spkrmlti.htm this should help u out n save u money

you may have burned the channel you were using..try taking the cover off the amp and checkin for burned spots or any wires that may be loose or touching within the amp.

If you see smoke, it's virtually always the power supply transistors. There are several things that can cause it but sometimes, they simply fail. I will generally work with people who want to repair their own amplifiers but the this JL amplifier is complex and not always an easy amplifier to repair.

If you can't find a local repair shop to repair it, you'll have to go through an authorized JL retailer to have it repaired by JL.

Let me know if you have any other questions.

This sounds odd, but try putting your subs out of phase from the mains. Just see if it changes anything.