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I purchased the infinity reference component system.

I understand how to wire the speakers to the cross over that it came with, but i'm curious about the wires currently in the vehicle for the tweeters and door speakers.

I have 2 green/yellow wires for the positive side that go into the door speaker and then 2 gray/red wires for the negative side....? I'm thinking that i will only need one of each into the main input for the cross over?

 
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That would depend on what those wires are actually doing. If I read it correctly, you are saying there are 2 sets of wires coming into the mid-bass driver. If this is correct, one set would be an input, and the other set would run to the tweeters. (kind of as a pass through)

If that is accurate, you need to find out where the inline crossovers are. If they are mounted on the drivers, then figure out which set is the power input from the head unit and wire that pair to the new crossover. I would then run a new wire set up to the new tweeter. If you choose not to, again make sure you determine where the crossover is for the tweeter. Could be inline, could be mounted on the driver. Make sure you don't use it as it may not be the right cutoff for the new tweeters.

 
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Awesome, thank you I'll check when I get home.