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On some brands depending on the speaker chassis you have to hog out the inside of the plastic housing some.
On JLs we use the JL grill as is is a nice look. It was the Alpines that had grills that looked like space ship parts so we installed the factory grills bay making some small changes to the speaker chassis and then using an O ring to get them to snap and stay in place.
We run the iPod cable down to the fuse box area and then to the cubby box on automatics.
Normally we would never run wires across that area, or under carpets and would do it the way you suggest, but for one iPod cable that is easy to tuck out of the way for gearbox service, we let that one pass, but only on automatics with the full console.
On 5 speeds you have to go the long way round as you suggest with an extension. In the Alpine parts we use I have never seen a slow down with extension cables... yet.
Hope that helps.