4 Channel Amp install

I'm going to be installing a 4 channel amp in my civic. when i bought the deck, (from a person not a store) they had it hooked up to a 4 channel amp. the way they had it set up had the speaker wires coming from the amp were running through the car to behind the deck and then it was spliced into the wiring harness in the back of the deck, so the signal ran through the factory speaker wiring. I'm wondering if there is any big advantages to doing this as opposed to just running new wire through the car directly to the speakers. also, if i do just run the wires to behind the deck, is there anything else i need to know?
thanks
andrew

The biggest advantage would be time (much easier, less work).  If you do this, just don't connect the wires from the radio to these as well.  You can just imagine the number of people who will ask if they can use their radio and their amplifier to power their speakers and get more power.

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My ex once told me I have a perfect face for radio.

cool. thanks a ton man.