Unless you are driving huge amounts of wattage into gigantic speakers, the factory speaker wiring is probably just fine. The only place you would need to run new wires is where you need to get the speaker signal routed from the amp up to the factory speaker wiring harness.

Some people even do a piggyback trick where they connect the amp from its location in the trunk directly to the rear speakers, then use the factory rear speaker wires to get the front speaker signal up into the the dash so they can daisy-chain them into the front speaker connectors. That way, you only need to run power/RCA/ampremote back to the amp. Although there is a lot to be said for running extra wires back to the trunk while you've got the car apart anyway.