I just sold our 2003 Saab 9-3 last Friday, partly due to my frustration with the audio system in this vehicle, so I know what you are going through. When I embarked on a procedure to correct the terrible sound present in the 9-3 early last year, no one else I knew of had done it. No information was available online, so I figured all of this out on my own. Here is how your system works:
The head unit has an internal amplifier, which provides mids and highs via the L and R front dash speakers, and rear deck L and R rear speakers. The Pioneer factory amplifier under the driver seat is connected via fiber optic cable from the factory deck, and it provides mids and highs via the front door 6.5" speakers. I never took the time to check what the center dash speaker is powered by, but in retrospect, I should have--I will explain why later. I am almost positive it is provided high frequencies from the external amplifier under the driver seat, and not from the head unit's internal amplifier.
Let me explain what I did, to perhaps help you in your decision-making process. My girlfirend wanted the use of the stock stereo, so stock appearance would be preserved, and so the Infotainment system and car computer would function. Unfortunately, this is all tied together via fiber optic cables, so taking the deck out will render a lot of stuff useless if you have those features.
I chose to use all JL Audio equipment--a JL 300/4 for mids and highs, a JL 250/1 for the sub, JL 6.5" XR Components in the front, JL 4" TR Coaxials in the rear, and a JL W3 12" subwoofer in a custom-fabricated fiberglass sealed enclosure in the trunk. For signal transfer, I used an Audio Control LC6i, which sounded like a great idea, given the signal summing capability of this unit. Since the front dash and rear deck speaker outputs from the factory deck do not have any bass frequencies, and the door speaker outputs from the external amplifier under the seat do not have any highs, I figured the signal summing feature would provide a clean, full range signal for my 300/4 to use.
But here is where it starts to gets tricky:
The blinkers/hazards audio output (clicking) actually runs through the front dash L and R speakers, so first off, don't even bother tapping these channels for signal unless you want to hear an amplified "POP, POP, POP" every time the blinkers or hazards are activated. The rear deck speakers are clean, high-level, mid- to high-frequency channels, though, so I used these channels along with the signal output from the door speaker amplifier under the driver seat to provide a full range of signal to the LC6i. From the LC6i, two channels went into the 300/4 and two channels went to the 250/1.
I thought for sure this would sound incredible, and it did, compared to the factory setup, but overall, I was not impressed. Here is why:
One thing I did not take into account prior to planning this installation was the fact that, even with the vehicle off, there was a slight humming noise present from the speakers. This, I theorize, was some kind of feedback from the fiber optic signal from the factory head unit being amplified and then played through the 6.5" door speakers. It's not a big deal in the factory state, but after that signal is converted to RCA format via line output conversion, then amplified, like in the system I built, it is definitely a lot more noticable. Also, since I was summing two levels of factory speaker-level output--one amplified more than the other, it was nearly impossible to balance the signal without introducing noise or lose frequencies--I had to constantly pick the lesser of the two evils.
I tweaked and fine-tuned the system for over a year, but could never get it to a point that I was satisfied with. Then the factory amplifier under the driver seat started going out, so I finally got fed up with it and used this as an excuse to put the car back to stock and sell it . So you know what I did to give my girlfriend a nice sounding system? I bought her an IS350 and sold the Saab to someone not so demanding as myself.
One thing I had not thought of until well after the point I decided to put the car back to stock and sell it was this: IF the center dash speaker is powered by the amplifier under the driver seat, it may be possible to use it as a high-frequency signal to sum with the low- and mid-frequencies of the door speaker outputs, and though you would lose L to R signal separation, you may have a cleaner high-level signal to sum into a line output conversion device for amplification than what I had using the rear channels.
But, in any case, I would offer the following:
If you are willing to lose the factory Infotainment and computer functions, and fiberglass a mounting kit from scratch for an aftermarket deck, clear, crisp sound is definitely in your future. Since you won't be dealing with the factory frequency and noise issues, you won't have any of the problems I had.
If you want to keep the stock head unit, you can simply tap the L and R speaker outputs from the factory amplifier under the driver seat, and the center channel (if it is there too), and convert those signals to RCA. I don't know that I would recommend doing without the factory head unit's high frequencies via the front dash and rear deck speakers though, because even IF the center channel is usable for amplification, you may have noise due to the feedback present from the factory Pioneer under-seat amplifier, and will definitely lose discreet L and R signal--which a lot of current music uses. From there, amplifiy replacement 6.5" speakers in the doors, add 6" X 9" speakers to the rear deck, and add a sub using your Alpine 5-channel amplifier. Keep all of the front dash and rear deck speakers in place, or replace them with better ones.
Hope this helps...Let me know what you do, or if you have any questions.