[johnneilson]

If you want the Main switch to kill the running engine you will need a switch with more than one circuit

Here is description from such a switch;

Master Battery Cutoff Switch with Alternator Protection
Click for a larger picture of Master Battery Cutoff Switch with Alternator Protection
This switch has three sets of contacts for cars with alternators. The main contacts disconnect the battery while the auxiliary contacts disconnect the ignition coil and short the alternator output to ground. A 3 ohm resistor (included) provides a load to protect the grounded alternator. A removable actuating key with splash guard, weather-proof cap, resistor and installation instructions are included.