My Challenger goes to the strip, battery is located in the trunk so I need a cutoff switch. The only things on the battery side of the switch is the battery and the alternator, so the switch will kill the motor. Even With the switch off, the battery discharges? What can I do?

One of two things, you have a bad battery or some thing is hooked up that your not seeing Is there a Volt meter hooked up to the battery? If so put it on the load, on, side of the switch
I sold one of my old drag cars to a friend, he hooked the volt meter up on the battery side of the cut off switch, which would kill the battery pretty quickly, 3 to 5 days with nothing else on

Had same problem last year. Alternator had a bad diode. Would drain battery over night.

Alternator