You definetly have it wired wrong. When I relocated my battery to the trunk I hooked up any wires that where on the positive terminal to the alt and then ran a 4awg wire to the rear of the car. If you are attempting to add a cut off switch ...........it should be in series with the wire coming from the alt to the rear of the car "your new batt feed".

ALT>4awg conductor>cut off swicht>battery
I hope that made sense.