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.
2012 F150 EcoBoost, 2005 Mustang V6 Convertible, 2011 Nissan Juke (wife's)