How do I prevent my 4 channel amp from cutting out when the music is loud?

Setup: In a 2006 dodge stratus I have 2 JL audio amps. 1000x1 350x4. kdc-x994 Excelon deck. A 12 inch W7. two mclass memphis 6.5' components in the front and mid level jl audio 6'9s in the rear. I have a yellow top battery and i also have a marine deep cycle battery in the rear(hold 101 amps). Big 3... show more Setup:
In a 2006 dodge stratus
I have 2 JL audio amps. 1000x1 350x4. kdc-x994 Excelon deck. A 12 inch W7. two mclass memphis 6.5' components in the front and mid level jl audio 6'9s in the rear.

I have a yellow top battery and i also have a marine deep cycle battery in the rear(hold 101 amps). Big 3 is done, all 0 gage wire. There is 4 gage wire going from both my amps and they are bridged to a 0 gage which runs to the battery.

Problems:
When I turn my car stereo loud, my system plays fine for about 2 or 3 songs and then the 4 channel amp will begin to cut in and out(I listen to hip hop music with A LOT of bass). I However this only happens when I am driving the car, when I am stationary it seems to play normally.

I also worry because when I first installed this the computer system in my car blew out and I do not want this to happen again, as it cost me $1000 to fix it. I think it blew out because my battery is behind my tire and instead of hooking up my amps to my battery directly, they hooked it to the fuse relay box(where you would place jumper cables. The first time I did not have a Yellow top though, i had my stock battery.

Please help, I dont want my music to cut out and I also can not afford to blow out my computer again! Does anyone know my problem?
Update: I got back into the car after posting this and after being out of the car for about 4 hours it is even worse. Now, if I even turn up the volume too high it goes to playing the Sub exclusively. But if I turn off the sub woofer, the 4 channel will play loud with no problem. I understand the sub my be overpowering... show more I got back into the car after posting this and after being out of the car for about 4 hours it is even worse. Now, if I even turn up the volume too high it goes to playing the Sub exclusively. But if I turn off the sub woofer, the 4 channel will play loud with no problem. I understand the sub my be overpowering the other causing it to protect but how do I fix that? do they need their own wires to run to the battery?

I also am going to buy a capacitor, any recomendation on one for this situation?
Update 2: Also, I opened all the windows and dropped my seats down(amps are on the back) and it is still an issue, I dont think they're over heating.
3 answers 3