I've managed to hit the window kill switch before now and not realised it. Could be worth checking for the window problem. Where did you wire the amp into? Straight from the battery or from under the dash somewhere? Could you have shorted something. Only reason I ask is on two circuits, indicators and speakers, if the hazard switch is removed it kills the indicators completely, and if you've got a speakr wire earthing onto the bodywork in the door it kills the stereo (no sound). Could be the same if you've tapped into something major. Normally I'd disconnect the battery again and retrace my steps
Good luck and if you're not sure go to a pro, electricity can be nasty, painful and expensive!!!!!!!!!!!!!!!!!!!