Why is my system shutting down?

Ah... NO!  You are saying you have three 2-ohm loads in parallel at your amp.  This is a gross overload on that amp as it results in a net 0.666 ohm load.  No wonder your system is shutting down, and I guarantee it is clipping like mad.  Keep operating like that and you will destroy your speakers and might fry the amp too.  You need to re-wire for at least a net 2-ohm load.  With 6 speakers @ 4-ohms SVC, the best you can do is wire for a net 2.666 ohms by connecting all three subs in each chamber in parallel (resulting in 1.33 ohms) and then connecting these two sets in series to the amplifier (totalling 2.66 ohms.)  This is the best way to use the system you have.  Then you can properly set your gain control... and I assume you are using a low-pass filter on the amp or externally?

Ah.  "Q-factor" in this case has to do with the electronic crossover.  It basically adjusts the rate of change at the peak of the crossover envelope, and in some cases the bandwidth of the filter.

DYOHN thankyou sooo much!! I cant believe how much of an idiot i am! I had each 3 subs wired in series for a 1.34 ohm load and the other 3 also wired in series at 1.34 ohm load before i had my jbl amp on them and the whole time i thought that was a 1.34 ohm load on the amp. I didnt know that you added the ohmage together and thats what the amp was handling. So I should wire my speakers the old way then? for  2.666 ohm load on the amp. When you say to connect the 2 sets of wires to my amp in series, do you mean to connect the positives to the positive on the amp and the negatives to the negatives on the amp?

OK and about using a low pass crossover on my amp. Don't all mono amps have a low pass filter already built into them? Other than that i dont have any external crossovers on my system. Would this be a smart thing to buy? Please inform me on what else I can do to enhance the sound of my system. I also have a subsonic filter on my amp. I have this turned off because since my box is sealed i dont think my subs are going to go too low that they will blow. Is this ok that I have it turned off? Alright thats pretty mcuh all the questions I have. Thankyou everyone for your help, you guys just saved me $1,000+ because thats how much i spent on my amp and subs together. No warranties.

Yes, you need to re-wire so that the three speakers in each chamber are in parallel, and then the two sets are in series with each other.  I did a little drawing that may help you.. And you need to activate the low-pass filter on your amp and set it to somewhere between 80 and 120Hz.

I went ahead and wired my subs like i thought dyohn had told me, but it ended up being wired like this  ... [URL=https://imageshack.us][IMG]https://img284.imageshack.us/img284/7188/oldwiringdiagram0pm.png[/IMG][/URL]

I played my system for about a couple minutes last night and no wierd scratching noises happened at all. I went ahead and started my car this morning to pull it back out onto the driveway form the garage and the subs would play fine. I wanted to hear how my system sounded with the wall layed down flat facing up in the back. I then turned on the car and a wierd popping noise happened from the subs when the amp turned on and then the subs wouldnt work. Both red and green lights from the mojo amp were on. Everytime i turn on the car the popping noise happens once. I went ahead and wired my subs to how dyohn said on the picture he sent and still the pop noise happens whenever i turn on the car. If anyone could tell me what is goin on i would appreciate it, thankyou