Have everything including alternator go through the switch to completely kill power to everything if needed. There's no point of putting a switch if your alternator is still connected directly to the battery.

 

well in the pic the alt. feeds the bat. and then the bat/alt feed to the switch, then the switch line to the fuse box. so the just bat. will feed the fuse box instead of the alt charging the bat. through the fuse box it will charge straight to the bat.

 

as I stated the diagram he posted will kill the alternator also, I used it before. hook it up like that start your car then turn off the switch the motor will shutoff.

 

NVM then, with a second look at your diagram I get it now. All it need to do is kill power to the ecu.