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Then if you hooked the aftermarket hu straight up to the wires behind the head unit, you most likely fried the stock Bose amp that is located underneath the passenger seat. It may be in protection, but I'm not sure if it has a protection circuit.
Basically what you did is send an amplified signal (speaker level) to the Bose amp which is meant to receive a low level audio signal (line level).
The stock Bose headunit produces line level outputs which feed to the Bose amp under the seat which then amplifies and processes the signal and sends it to the speakers.
If you bypassed the stock Bose amp and sent wires from the aftermarket head unit to the stock speakers, you would have fried the aftermarket head unit because the speaker impendences are 2 ohms. But I believe you did what I explained above this paragraph.
Your best option to fix this problem would be to buy an aftermarket amp that is stable to 2 ohms and hook it up to your stock speakers and run RCA's from the aftermarket head unit to the aftermarket amp. Keep in mind you will lose function of the stock "sub". I don't even know the impedence of it but I wouldn't even try to power it because it doesn't do much anyways and you'd most likely blow it.
There are many other options but that would be the best quick fix. You can try to replace the aftermarket head unit with the stock hu (reverse what you did) and hope that the stock Bose amp still works but if it does not, you can not avoid spending money to get your speakers working again.
2004 Mazda6 Sport GT
Injen SP6072P CAI, 3.7l TB, 3/4" IM spacer, EGR Optimization/Re-Route, Transmission Cooler + Inline filter, TB coolant bypass/T replacements, 35 watt 5K HID's in Low Beams and Integrated Fogs