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Ok. So I've done some research of my own now. I think I have your answer.
This is a quote from another forum, and it explains how to BYPASS your factory amp. Right now your speaker wires go from your head unit to the factory amp then from the amp to the speakers. The problem is that you're not powering the amp any more. So this is how to bypass the amp all together.
"""NOTE TO MODS: I just got this idea while posting a long-winded reply about the subject in another thread. This question seems to come up quite a bit. Any chance for a sticky? Thanks - JP
Quite a few people have asked about replacing the factory speakers with aftermarket ones and how to power them off of an aftermarket deck, which inevitably brings up a bunch of concerns about how the impedances are different, and the potential problems that this can cause for the speakers and that factory Monsoon amp. For those that want to install aftermarket speakers without having to worry about all of that, it's a fairly painless process to bypass all of the factory amp wiring and remove it from the equation. This way, you can install pretty much any aftermarket speakers that are meant for the car with no impedance issues to worry about.
In your trunk, behind the left side carpet, there's an amp and a wiring harness that plugs into it. Pretty much every wire is either an input from the radio, or an output to the speakers.
This thread has the list of pinouts:
Monsoon System Pinouts
To bypass the amp: unplug the harness, match the input to the corresponding output for that speaker, and connect them at the harness. For example, if you wanted to bypass the amp and have the headunit directly connected to your new door speakers, you'd want to connect:
E2 TAN Left Front Speaker Output (+) to E15 DK BLU Left Front Midrange Speaker Output (+)
E3 GRY Left Front Speaker Output (-) to E16 LT BLU Left Front Midrange Speaker Output (-)
E1 LT GRN Right Front Speaker Output (+) to F7 ORN Right Front Midrange Speaker Output (+)
F1 DK GRN Right Front Speaker Output (-) to F6 DK GRN Right Front Midrange Speaker Output (-)
Just strip a little bit of wire away and jump them. Or, cut them from the harness and splice them together.
Now for the rears, you want to do:
E5 DK BLU Right Rear Speaker Output (+) to F14 DK GRN Right Subwoofer Speaker Output (+)
E4 LT BLU Right Rear Speaker Output (-) to F13 LT BLU/BLK Right Subwoofer Speaker Output (-)
E6 BRN Left Rear Speaker Output (+) to F15 DK BLU/WHT Left Subwoofer Speaker Outlet (+)
E7 YEL Left Rear Speaker Output (-) to F16 LT GRN/BLK Left Subwoofer Speaker Outlet (-)(NOTE: This was all pulled from the Monsoon Pinout link I posted above.)
At this point, you'll have 8 pairs of spliced wires (+/- for each of four channels). Leave the harness disconnected, and you can now remove the Monsoon amp and toss it in the trash, burn it, sell it on eBay, etc. If you use a correct wiring harness when you install your aftermarket headunit, all of the outputs from the headunit are now directly connected to the door speakers and the rear deck woofers. You can now install any set of speakers you want, as long as they're meant to go in a car, and are 4-ohm (ie pretty much everything except Infinity Kappa).
Good luck!"""
Just read this carefully a few times and ask any questions before you cut anything up
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