Why does my system sound terrible?

First off I have an '06 Scion TC.

I am using the stock headunit run into an Audio Control EQX and from there into a 50x4 Memphis amp and an 1100x1 Memphis amp.

The speakers in the front are Boston Acoustics Pro 60s and the speakers in the rear are just the stock Scion speakers. The sub is an Adire Audio Brahma 12D2 wired for 1 ohm.

The problem is that the sub is very quiet and the woofers in the doors are trying their hardest to play below 50 hertz, which isn't working out too well for them. The EQX won't let me adjust anything that goes to them below 120 hz, and Bostons crossovers seem to assume I wouldn't think of letting any low frequencies get to them to begin with so they don't do anything about it. The sub also refuses to play anything below about 40 hz, and occationally will produce a very horrible popping noise like its trying to excurt about 3 feet even though it's pounding out a massive 75 db.

I know I'm probably going to be told to get a real head unit, but if there is any way around that I'm open to suggestions.

I've actually been wondering how to check the crossover settings on the amps. Memphis was nice enough to label one side of the knob as 20 and the other side as 20k with about 2mm of adjustment between. Am I going to have to take it to someone with an RTA and just check it with a test CD?

You are correct about the gain being pretty high, but even with the EQX maxed and the gain turned to about 75% the bass just isn't there.

Sadly in the end I think I'm trying to sew the proverbial silk purse. I was really hoping the EQX would take care of all my needs, but garbage in garbage out it would seem.

Anyway, thanks for info DYohn. 

Also, if anyone knows what voltage I should set the mcd1000 to for the Brahma, I can do that tonight to see if I still get the popping. The amp is 1100 watts and the speaker is wired to be 1 ohm, but I can check the exact measurement when I get home tonight if it makes a big difference.

Ohm's Law: Power=voltage squared times resistance.  1100 watts is delivered into one ohm at 33.16 volts.

How is your EQX connected to the factory HU?  Also, many factory HUs include EQ that cut off the lowest frequencies and emphasize other bands to compensate for shortcomings in the cheap factory speakers commonly used.

From the factory HU the speaker outputs are run into the EQX, which as far as i understand just amps them up and sums the front and rear to give you a sub output.

Can I use Ohm's law for the components also, or does it only work for the sub?

Also, about setting the crossovers on the amps. Is there any way to do that without an analyzer and a CD with some sweeps on it?

Ohm's Law is a universal electrical truth.  You need to setup the EQX first, then set the amplifier gains.

The EQX is a very powerful tool and can be difficult to get setup correctly.  First off, do you have the owner's manual?  Did you setup the input levels per page 13-15 of the manual?  Also, if you ar using the subwoofer output, the EQX has a built-in subsonic (or high-pass) filter set at the WAY too high value of 33Hz, which means it will not pass anything lower than 33Hz.  There is not much information down that low, but it could be part of the reason why you think you are missing something.  The sub output low-pass is preset to 90Hz.  SO, on your subwoofer amp, you'll want to disable the amplifier crossover, or set it to LP and the highest setting it has.  I suggest using the EQX full-pass output for your mains amp, and set the amplifier's crossover to HP (high-pass) and adjust the pot to about 90Hz.  When you set your amplifier gain, press the bypass button on the EQ.  Then when you adjust the EQ, be very careful using the boost.  It is better to cut than to boost.

This helps me a lot, I had just posted about my HU dilemma prior to reading this. I was thinking of doing a similar style of set up (with not nearly the components mind you) but off the factory HU. Would the JL clean sweep actually fix all this the way it says it does on the website? How much was that Audio Control EQX? Are ALL HU's guilty of this or are some better than others? How can you find out (from literature, I don't have access to that kind of equipment)?

Wow thanks for all the info guys. I do have the user manual for the EQX but opted to bring it to a local installer who has a lot of experience with them. Once he mentioned opening it up and maybe replacing some chips inside I knew it was out of my hands.

I bought an Alpine CDA 9856 to replace the stock HU. It was a pretty great deal for $190, and the 2v preouts won't be a problem with the EQX. They didn't have the dash kit in stock so I can't install it until Saturday, than I will visit the local EQX guru some time next week when he has some free time.

I shall let you all know how it turns out.

And once again, thanks for the great input.