Yes. You need to put a 1K ohm or so resistor in series with the connection from the headunit to the factory sub amp. This is a fairly well known issue and has been discussed here a few times.
Some say to use a 5V regulator instead, but the resistor works just as well and is simpler and more reliable. It limits the current that rushes into the factory amp turn on input. The factory amp is expecting a 7V or so signal, but most after-market units put out a 12V signal.
To be clear, connect the turn-on signal from the headunit to one side of the resistor, and the wire to the factory amp to the other side. A 1/4W or higher resistor is good for this. You can get one at Radio Shack. Catalog #: 271-1321 is one example.
