Chris,
It all depends on where you mount your amp/powered sub. If you plan on mounting it in the back then splice the lineout converters to the speaker wires in the back. This way you will not have to stretch long amounts of rca cables. The shorter the rca cables the better to avoid line noise. I'm not sure there is a remote turn on for amps on the stock radio so you might have to run a wire from any point where you can get +12V when you turn the key. the cigarette lighter will work or you can do what I did and run the wire from the fusebox and attach it to the ACC fuse then run it along the bottom trim of the car to the back if that is where your amp is.
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'01 Alpine Green SE
"Screw milk, got Xterra?"
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'05 Silver Off-Road 4x4
"Screw milk, got Xterra?"