You can buy a harness that will connect right up to most aftermarket radios and your sub (anywhere from $6-$15 dollars; at most car stereo stores or online). I went through this same process when I got my ST. The problem with this is that the factory sub does not use a 12 volt source. When I tried using a 12 volt source, I would get a pop through the sub every time I would start the vehicle. The factory sub only requires a 5 volt signal which is what the factory radio would send to the subwoofer. If you try and use the aftermarket harness which powers the subwoofer from you radio, you'll send 12 volts to the subwoofer. It's the 12 volts that causes the pop sound. If you were to install the following
http://www.sminntech.com/ampinterface.html
the popping noise will cease and you will have a proper functioning factory subwoofer.