If you're gonna be putting in aftermarket speakers as well as aftermarket amps you can still use the existing speaker wiring, you'll just need to be able to access the infinity amplifier because that's where the bypass will have to take place. I'm not sure exactly where the infinity amplifier is located, but try under one of the seats or behind the dash somewhere. A lot of times you can hear a clicking noise when you first turn on your factory system. Try to locate that clicking noise because that's actually the relay in the infinity amplifier, so if you can find where the noise is you'll find the amp.
Once you've found the amp, you'll have to figure out which wires are the speaker wires. You should use a multimeter to first determine the constant and switched power wires, as well as the ground wire, and just make sure you don't mess with any of those. A lot of times the amp will have a plug for the power and ground and signal inputs, and then another plug just for the 8 speaker output wires. Or they may all be in one plug, but either way there will be a total of 8 signal input wires and 8 signal output wires and they will need to be cut and connected directly to each other (thus eliminating the infinity amplifier).
If you use a multimeter you can check for resistance between different pairs of wires and when you get a reading of approx. 4 ohms you know you've found the amp's speaker output wires that lead directly to the speaker's positive and negative wiring terminals. Then to figure out which speaker each pair of wires goes to you can use a speaker popper. Finally, for polarity plug the harness back in to the amp and turn the system on. Check for voltage across the pair of wires--positive voltage means the wire touching the red test lead is the positive speaker wire, and negative voltage means the wire touching the black test lead is the positive speaker wire. Continue to do this for the remaining 3 pairs of wires.
Make sure you do that resistance check first though because it's important that you get the wires leading directly to the speakers and not to the head unit or into the amp. Only the wires going straight to the speakers will give you much of a resistance, let alone the 4 ohms that it should read. Because once you use the speaker popper, if you've accidently picked wires going to the head unit you could damage it. The speakers can handle being popped just fine, but not the head unit and/or amp.
Now to determine which of the wires are the input wires on the infinity amplifier, you can use a test speaker and turn the head unit up to about half volume and just start trying out different pairs of wires until you hear sound coming from the test speaker. you'll have to listen very carefully because it might be hard to hear it, but once you've found a pair you'll hear sound come through your test speaker. Then, use the fade/balance control to determine which area of the vehicle (front left, front right, rear left, rear right) that particular pair of wires goes to. And then for polarity just repeat the process I described above for the infinity amplifier's output wires.
Just FYI the infinity amps use a high level input signal which means that technically you can use an aftermarket head unit with no problems as long as the factory amplifier gets a proper turn on signal like Jeff mentioned above. However, since you have aftermarket speakers and are also gonna power them using an aftermarket external amplifier, you can't (and wouldn't want to) run the signal through the factory amp like might be the case if it's just a head unit. This is because the infinity amps can only handle a limited amount of power going into them, before they will distort very easily; needless to say an aftermarket external amp will present way too high of an input signal for the infinity amp. Basically it'd be like amplifying the signal twice.
The remote turn on of your aftermarket head unit will need to be hooked up to the remote turn on for your aftermarket amplifier.
As for the dash 3.5" speakers, you shouldn't have to worry about those at all actually, because they're wired up in parallel with the door speakers. Once you bypass the amplifier like I described above, essentially both pairs of speakers are hooked up to the same 4 speaker wires in the radio's harness (these are the wires that should obviously be hooked up directly to your 5-channel amplifier). With the speakers wired in parallel they present a 2 ohm stereo load to the amplifier which it can handle very easily.
Ethan
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"Patience, persistence, and perspiration make an unbeatable combination for success"
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