Gadgetron

Good Morning, After a recent road trip (Boston to Detroit and back) I now feel the need to get new stero to intergrate the ipod into for my 2005 Outback Sport SE. Presently I am looking at getting this head unit http://www.tweeter.com/product/index.jsp?productId=2190544&cp=1124288.1124546.1124466&filter=yes&fCat=1124466&fbrandid=92340&fpricesort=priceAscending&parentPage=family I would end up running an stero to mini headphone jack into the AUX in-put to play my ipod. My plans were put on hold today because I found out that if i put an aftermarket head unit in place of the factory in dash CD changer, that my subwoofer will no longer be controled by the "new" deck. This would result in a muddy sub and thats not going to fly with me. Has anyone run into this problem before? is there a solution or am i stuck with the 6 disk changer? I really only wanted to swap the head units and not have to buy an brand new sub. This was A LOT easier with my last subi (97 Outback sport). Why has Subaru gone the path of making after market stero install such a pain in that rump roast? thank you for your help