Sorry.

I just reread your original post and figured out that I misunderstood it.

The guy at Best Buy is correct. They will need to bypass the external amp in order to hook up your new HU to the factory speakers. You can hook up your new HU to the existing factory speaker wires in one of two ways:

1) Tap into the factory speaker wiring and connect the HU to the taps.

2) Purchase an adapter harness that will plug into the factory harness on one side and the new HU on the other.

If they try to sell you on a complete rewiring job then go elsewhere because it's simply not needed. It may be necessary to run new power and ground wires but new speakers wires is overkill.