So I have a new pair of 6x9s to go with my sub and stuff and I went to go put them in and there are only two wires from my new speakers and the stock speakers have a connector with 4 wires. How do I wire the new speakers in??

You have a monsoon factory amp, it has crossover built in that powers your woofer and tweeter separately. These links below may help but search for Monsoon and you should find more if you need......

Replacing 6x9 Monsoon's
wiring diagram....go down a few where there is 4 rear speakers





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