That wiring is a right mess, would be really pissed if I had actually paid someone to do that. Does not look like the cause of your issue though.
I would however move the thin blue wire (probably remote power) away from the clip where the seat slots into.
Those MTX Thunder 5500 subs should have a 150-300 watt rms amp each (or a single 300-600 watt rms mono/bridged)
I presume the speakers are wired in parallel to make 2 ohms. So the amp will be running at its lowest possible impendence and still only be just about capable of running the two speakers that you have.
I imagine the gain is turned right up to compensate for the fact the amp is not powerful enough.
Over-driving the amp has two effects:
it can produce clipping which often leads to damaging the speaker (due to heat or over excursion)
it can damage the amp as it is always working hard and running hot.
Clipping, if you don't know is when the signal is clipped at the top of the sound wave as the amp has reached its maximum
Sounds like you should just turn down the gain and connect it to just one of the speakers.
Then I would get a another MTX Thunder 311D mono amp to drive the other speaker or get a 600 watt RMS amp to drive them both.