Okay so I'm not finding anything that's burnt. I did however check out to see if the headphones are working and they are on both channels. I'm assuming headphones go through the same channels as the speakers, so that would most likely mean there's a problem between the connection of the sub and the speaker wire right?
Found something that might be the problem, uploading pic. I haven't taken the board apart and am just looking around. Noticed this had a wire stickign out and looked a little brown.
http://i.minus.com/ijtjOI.JPG