Audio Systems: 98 ford expedition - radio electrical, little fuse, fuse panel

Question
Hello ,
I have a '98 expedition with mach audio system. I had added an aftermarket sound system but have decided to sell the truck. I removed all aftermarket components. I am trying to hook up the factory rear subwoofer again. The old one was blown so a different aftermarket sub is in place and hard wired as it has different hook-ups. I have wired it to the original amp. Now I put the OE radio back in and plugged the amp in. The radio worked fine but the sub was not. I disconnected the amp and in the process my battery had died so my old man put it on a charger. i left for a couple hours and he claims he started the truck with the charger still hooked-up (don't know if that can cause any damage) and when i came back the inside of the truck smelled like something electrical had shorted or burned up. I now get no power to the radio ( tested it and still works) and there is a little fuse panel under the hood by the fuse box with 5 fuses or so in it and number 3 controls the rear unit along with the cd changer and the radio. This was blown and when i try to replace it it immediately blows the new fuse. I have the amp, cd changer and radio disconnected and it still blows this fuse on contact. I am clueless.
Keith

Answer
the woofer needs to be original  or a 1.5 ohms woofers
aftermarquet don't work or sound good because they are 4 ohms

there are 2 amplifiers in the vehicle , one is for the 4 inside speakers and the small one for the woofer,
the short is in the big amplifier,
you can get a rebuild unit from oemautosound.com

good luck