Tuning a sound system in a vehicle 101
The car is an acoustic cavity. Each car has its own unique audio signature and you can see it on a Real Time Analyzer or RTA(which I will be talking about here). To see the curve in your vehicle, you can download on your iphone, a program called RTA by Studio Six Digital. This is by no means the one I would tune with but it will suffice if you don't have access to an audio shop with a real one. You can buy one for about $350.00 or you can get the serious one for about $1000 from Audio Control. Anyway, turn it on, go through the calibration. Then go to iTunes, and in the store search for pink noise. This is a recording of every frequency played at the same time. Put that on a cd, put in your cd player, turn the volume up and turn on the rta. You will see a curve, each frequency will be moving a lot, but within its own space and you should see a curve from left to right. That is the acoustic curve of your car with you in it. (Now why would I say that), because it matters when you are tuning.
Most of us audio people tune our cars without being in the car, because the body affects the curve. However, if we know were going to get judged by 1 or two judges, we will tune with the seats where they need to be, and with one or two people in the car so that the tune matches what will be in the car when it is judged. For you, normally, its either 1 person driving, or you can tune it outside the car, and it will be ok.
This curve is very important, because when adjusting the processor it is going to change, but the curve also shows us problem areas that we are going to have to deal with. Have you ever heard a base note in a car that just shook the windshield? That is coming from one of two places. Either from way too much sound pressure, or from the resonant frequency of the car. If you look at the RTA, the bar that is the highest using pink noise is the resonant frequency of the car. If ported subwoofer enclosures are your deal, you want to design an enclosure and port that stays away from this frequency. Ported enclosures based on diameter of the port and length of the port play 3db louder at the resonant frequency of the port, if that is the same frequency of the car, your bass at that frequency will be louder than everything else and will not be balanced, and you will not be able to fix it with the EQ.
Now, When you install your speakers, they need to be installed solidly. (Your saying, im screwing it into the factory location, isn't that solidly?), no. its not. If you hold a subwoofer in your hand, and turn it on, and play something that can move the cone a lot, It will be difficult to hold it steady in your hand. Now imagine mounting that in your car. The energy of the cone moving has to go somewhere. That is why home enclosures (The really good ones, are so heavy). You want all of the movement to come from the cone. If the transference of energy gets passed along to the metal in the car door, it becomes resonance. this is also distortion and unwanted artifacts being added to the music. This is where adding sound deadening to the door adds weight to the metal, and makes it harder for the speaker to transfer its energy. Us guys that do this professionally, will coat the entire vehicle from top to bottom. Even the trunk, It makes a big difference.
With amps and speakers installed, we need to check a couple of things. First The more signal voltage and the more power voltage that gets to the amp the better. What am I talking about? The battery on its best day, will only produce 12.7-13.5 volts continuously. If you read the specs on your amp, it will give you two power ratings. One at 12 volts and one at 14.4 volts. You want 14.4 all the time. It may require an upgraded alternator, but why buy an amp to get 100 watts per channel only to let your alternator force you into 75 per channel?
Signal Voltage. This is at the RCA input. Your amp will tell you how much voltage it can take. Most are 4 volts. Some are 5, 6, and 8. One or two are 10.

. The more signal voltage you can get into the amp the better but only up to what the amp will allows. If we use the signal level out of the factory radio you are doing good to get 2 volts. Now your new amp you installed is wasted. To get the snappy crisp highs, tight midbass and chest kicking sub-bass, requires a minimum of 4 volts at all times. You do this by adding a line driver for each RCA. The line driver allows you step up the voltage so you always get what you want and get your moneys worth out of your amp.
Now we come to setting the gains on the amp. This is complicated. You want the gain set to its maximum level before distortion kicks in. how do you do this? You need a scope, and a audio track playing 1hertz tone. When you hook up the amp to the scope, you will see the wave change on the scope. When it becomes distorted, you back that down, and your good to go.
Now, most people like to do the EQ at this point and I think that is probably one of the most misunderstood audio tools ever created. The EQ is the last item adjusted. You want to adjust everything before having to mess with the EQ. So what are you adjusting for are small corrections after everything else has been fixed. Start with the crossover before you play anything. You don't want to blow up a set of speakers. Once they are set, then play your pink noise again, and look at the curve. Pause it. Now, using the level settings in the processor and with a db sound pressure meter hanging from the rear view mirror, cut off everything but the tweeters, get a measurement, and then do the same for all of the midrange, midbass and so on, you want to adjust everything to be very close in output to everything else. The sub will be a little different but everything else should be very close. This will really help with the imaging. What your trying to do by adjusting the crossover, and levels is to have no more than 3db variation between each frequency. Adjust your crossover points, and slopes to try and get this as close as you can. Once you have done that enough, there should only be 5-7 frequencies that are still out of place.
Now using the EQ, look at the bands on the RTA. You never want to add gain to a frequency. Why? Because you are adding something that was not originally there in the recording. Use the adjacent frequencies and lower the gain to bring it into line. When done you should have a really smooth curve. Everyones curve will be different because not everyone will use the same speakers, not everyone will sound deaden the car the same. But the curve should be smooth.
When you look at where the sub is playing, it may be way out of wack. You can try to lower that frequency, but if it wont go, this is where you have to listen. If it sounds out a bit, you can try adjusting the crossover, putting a pad over the sub, adding wool inside the enclosure, but if all else fails, you may have to add a little gain to the adjacent frequencies to smooth it out. If you have to add more than 3db then just leave it alone.