Something is not right here. If you have the jump a properly wired car with the jumper cables in the correct location (in the back at the battery), you would not have much current going over the 20A contacts of the Moroso switch. It should be going to the solenoid. As I understand it, the kill switch is designed to isolate the battery from the rest of the electrical system. As a matter of fact, that is how the Moroso switch is described on Jegs.com.
As for having a 100A alternator, you still should not have much current going back to the battery. If you are pulling 20 A on that connection, you have a dying or dead battery.
If you are trying to use the battery kill switch as an overall kill switch, you could wire up something like the second picture. It would isolate the battery and kill the ignition. With the ignition cut, the engine stops, and the alternator stops with it.