To the 2 guys above me, I wish I knew half of what you are talking about haha. Me and my friends think putting 2 subs in the trunk, having an amp and some new speakers is like the best thing in the world. Well, I'm here to learn though.
I'll summarize. Car audio's issues are all because of the cabin. The most basic problem is that you don't own a Maclaren F1, and even if you did, I'd doubt if you'd waste the weight savings and install an audio system in there to struggle with the music of the BMW V12.
See in home audio you not only have a larger space where you might cover up most surfaces, including windows, but that you can sit in a spot equidistant between the two speakers you're using. In a car, you have to be able to drive it, obviously, but also since you don't have a Maclaren F1, you're sitting off to one side - that means your ears are inherently closer to the driver side tweeter(and midrange), then the midwoofer, then the passenger side tweeter, then the passenger side midwoofer, then finally the subwoofer. Tweeter(and midrange) placement is the first step to getting this right, but that's not straightforward. Depending on your tweeter's dispersion pattern and the car's cabin, if the tweeter (and midrange) are on the dash level, you get the driver side speakers too close to your ear and therefore pull the soundstage towards it, and the dispersion pattern might end up with enough of the tweeter's output bouncing off the windshield, making the sound more sibilant. You are not hearing a strong "t" or "s," or cymbals; you are just hearing the same microsecond-duration sound at different times - not enough to easily tell that they are, but enough to screw it up especially in this aspect. Putting them in the kickpanels next to the door-mounted midwoofer might put the soundstage below your eye level, which again is nothing like home audio.
The first step therefore is to install properly: find the optimum location for the tweeter and install it cleanly, and also to properly dampen the doors if the midwoofers are there. If you relocate them to pods in the kickpanels, they might be angled to image better, but also lose enough air volume and therefore lower freq response compared to dampened doors, which means you will depend more on the sub. This part is important - if you put too much frequencies into the subwoofer, it will then pull the sound towards wherever the heck it is, on top of it being farther away, so not only are you hearing its output microseconds later, but you'll hear it from the rear (which is not how it is in a real performance nor a home stereo) and feel like the bass is too flabby.
You've already did as much as you can with the installation, next comes the processor, which initially was just an EQ, then later a crossover, then the new digital processors currently in the market. This is very important as instead of, say, simply adding nice speakers that don't rework what's wrong with a car's cabin, it can apply the needed corrections. Foremost of these is time alignment. Input protocols in processors vary as some require putting in the microsecond delay, while some require only that you measure the distance to each speaker, and then it does the computations. Either way, the goal is that it should introduce a time delay to the speakers closest to the driver-listener, so the sound arrives at the same time. When this is done however that also means each speaker will need its own amplifier channel as the processor will output 5channels or so of analog sound with time delay applied, so that means it must also apply crossover filters to set what frequencies go into each amp channel then to the speaker. Gain structure can then be reworked at this point - having matched them for distortion, now you can level-match the output of the processor going into the sub and tweeter so they will all be coherent with the midwoofer. If your tweeters are too loud for example then there's no EQ that can be broad enough to trim all of its frequencies. If you buy a speaker set, the passive crossover usually has as part of its circuit some way to attenuate the output to the easier-to-drive tweeter; in an active system you must do this with the processor and amp. In my car I have a -8db output on the Vifa tweeters from the processor and 0 gain on the 75wpc amplifier to match the 150w amp at 12:00 on the knob powering the Focal midwoofers (it's a four channel, asymmetrical amplifier by the way).
Done right and you might not even have much to correct using the EQ (I don't use mine anymore). At some point people were able to get closer to the sound of a home audio system* so some people decided the challenge to doing so would make excellent competition, so now we have EMMA and IASCA judging the imaging accuracy and spectral balance of each system in competitions. Part of the fun are the restrictions - for example, a speaker mount must not change the shape of the A-pillar as far as the driver's field of view is concerned, so minus points already for the huge home audio tweeter in my car (I don't compete and it doesn't obscure my vision so screw it).
In any case, you might want to go over to www.diymobileaudio.com to learn more about car audio. What I posted up there isn't necessarily the most accurate workflow for setting up a system but they can help you better over there. I've been avoiding car audio forums because I haven't really finished the one in my car, and with the possibility of leaving to do my PhD in the works after my MA degree, I just don't want to sink money in it anymore. Wherever I move though if I have a car I'm likely to install a simple system in it using an integration processor (takes speaker output from the stock receiver as an input, then sends it through the ADC, then processor, then the DAC) and kickpanel speaker installation that won't mess with warranties.
*They usually refer to a full size 2ch system, but as far as I'm concerned, it's closer to a near field monitor system (because it is nearfield and the soundstage is replicated on the dashboard, like on a desk).