Be very carefull not to screw anything up here. Your playing with fire, literally. Your wiring and batteries can handle hundreds of amps. You can electrecute yourself, fry your cars electrical system, set fire to your car, fry your new stereo system or have a battery exlplode in your face and blind you by spraying acid in your eyes.
Just be very aware of the dangers. Those batteries are always live, and the alternator wire is live when the car is on.
Be very carefull not let any bare positive wires touch the cars body/ground and be carefull to not allow any tools to touch both battery terminals (this is surprisingly easy to do).
It is best to do all your electrical wiring with the battery negatives disconnected and fuses removed, and only attach grounds and install fuses when your certain all your wiring is correct. Which in your case we know it's not.
Double and tripple check everything before you connect those negative terminals and fuses.