I just replaced my old terminator 12" subs with two new 12" jl audio w3 4ohm subs and the mtx terminator amp keeps shutting off and flashing red. I kept everthing the same from my original mtx terminator purchase just switched out the subwoofers. What can I do to fix this problem?

Based on your setup, I would recommend wiring your JL W3v3.4 subs in a dual 2-ohm configuration. This will result in a 1-ohm load to the Rockford 1500.1 amplifier, which is within its safe operating range.
To wire your subs in a dual 2-ohm configuration, you would connect the positive terminal of one sub to the positive terminal of the other sub, and then connect the negative terminal of one sub to the negative terminal of the other sub. Then, you would connect the positive and negative of the combined subwoofer terminals to the positive and negative terminals on the amplifier, respectively.
Here's a diagram to help illustrate the wiring process:
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+ Sub 1 + ' --- ' +-------+-------+ ' ' + + ' ' + Sub 2 + Positive from Sub 1 -----> Positive from Sub 2 Negative from Sub 1 -----> Negative from Sub 2 Positive from Subs -------> Positive from Amp Negative from Subs -------> Negative from Amp
Keep in mind that you should always double-check your wiring with a multimeter to ensure that you've wired everything correctly and to avoid damaging your equipment. It's also a good idea to consult the owner's manual for your amplifier for specific instructions and guidelines on how to wire your subs.

This site well be helpful for you to configure the connections
http://www.the12volt.com/caraudio/boxes.asp

Take both positive leads to the positive of the amp. Both negatives from the sub to the negative of the amp. Utilize the bridged output connections. This would present a 3 ohm load which would be around 100 watts rms (rough estimate)

your aux cords could be craked or cut somwhere

the amp is under to much pressure get a bigger 1

You should definitely upgrade the power wire to the sub amp to 4 gauge -absolutely your choking your amp its starving for current-poor thing is starving !!!!!!!

you may only be able to get but so much out of the subs. If you turn the bass down a little so the that you dont drive the subs so hard you may get a little more wattage out of them

HI DUDE .. U CAN ONLY SINGLE PC OF JL SUB BY BRIDGE MODE ... COZ UR MTX AMP HAVE 300WATTS RMS ....

the amp is no where near strong enough that sound you hear is called hard clipping and it will destroy your subs in minutes. depending on what model JL subs you have I can sell you a better amp.

I had same problem with a TC6001 and get solution from MTX, not send to MTX instead MTX kindly sent a quotation for parts to be replaced, I can tell you what parts need to be replaced if you still need a solution.