IT NEEDS TO GO IN THE GROUND WIRE.
Both will keep it from starting but if you have an electrical issue and want to kill all power quickly it will not kill it if it's running. The alternator will continue to feed the juice.
Put in in your ground.
As a side note, this (& my lay-out) isn't legal in NHRA drag racing. Their rules require it in the positive cable, AND turning it off has to kill the whole car - not just the engine. Lots of creative wiring strategies out there to facilitate that. I won't argue the stupidity of their positive requirement, because it is.
Also, if you have anything like remote power door locks, turning the battery on and off by the ground wire can cause those to cycle unless you supply that system with a ground that by-passes the kill switch. Ask me how MISF knows this.......
For just the purpose of isolating a second battery and the winch I'll suggest a marine battery bank switch instead of a kill switch. These are also designed to pass the high intermittent amperages common in starting & winching. I've seen up to 1000 Amp ratings for these.
Then bridge across the two battery bank terminals with a Blue Seas Automatic Charge Relay (ACR). The switch will allow you to select either battery or both, or none. Then as long as the alt's charge wire (& any other charge wire like from a trickle charger used during long term storage) is connected to the switch's load terminal the ACR will first charge the starting battery and
then the secondary or 'house' battery.