Your subwoofers should work just fine now!
I just installed a Kenwood DNX6190HD in my 05 Mustang convertible (has the Shaker 500 system). All my factory speakers work, including the subs and amps. I used a Metra harness and voltage convertor I got from Crutchfield.
Well, since I posted this originally, the passenger door speaker has started to cut in and out, and the sub on the same side is barely pushing at all. Something is definitely up with the setup and I suspect one of the factory amps is fried/not working properly.
I have a pair of the Shelby/Kicker 8" woofers coming in the mail tomorrow and have an appointment next week at an installer to swap out the factor 8's, the front Pioneer 6 x 8's, and the two factory amps for a single higher powered amp, as well as dynamat the ever-loving bajeebus out of the doors. I'm not sure on which amp to get, since I can't find much info about the Shelby/Kicker 8's online. I will see what the specs say when they come in. I honestly don't know much about car audio at all, so I'm kind of at the mercy of the install place, but they've been around since the 90's doing competition and whatnot, and the owner seems to really care about customer satisfaction/saving money, over pushing $$$ down people's throats.
If anybody has a suggestion on what amp to get I would be glad to hear it. I'm not going to be running any subs in the trunk - I need my trunk space. I'm also hoping to be able to hide the amp somewhere because I'm going for a "stock/classic" feel for my baby and I don't want to open up the trunk and be like "oh look...amp..."