You need to register the battery if you changed it out if you replaced it with the exact same AH battery. Otherwise it has to be registered and that AH rating changed to what you have.
However I would charge the battery and take it to a parts store that can load it and see if it is truly DOA. You don't need to do anything when removing the negative post but if it was disconnected a long time you might well have some issues but not everything being dead.
Is it possible the sub install is drawing pwr and causing a huge parasitic load?
You can check if this is true however by putting your VOM between the neg post and the neg cable, neg cable not connected. Allow the car to go to sleep and measure the amp draw. Our cars should not draw more than 40miliamps but could be a bit higher since ours are so heavy in the electronics area. However if you see say 100miliamp or more you have something drawing pwr that should not.
Hope this helps some...