So I think maybe a little more detail about my situation would help clarify my question. This is what my rover looks like.
Right or wrong, the way I designed it was to have all of my “power” electronics separated from the Pixhawk, GPS receivers, compass, etc. to prevent any magnetic interference. In that picture you can see the top box has the Pixhawk and GPS receivers, and the box on the back has the BEC and Sabertooth motor controller.
The idea was to segregate all of my wires carrying large amounts of current away from my compass.
The problem is that the ideal place for the emergency stop button is right on top of the box with the Pixhawk, GPS receivers, compass, etc. And what you guys are saying (correctly in my opinion) is that the emergency stop should cut off all power to the rover, or at least power to the motors.
This means I will need to run one of my large current carrying wires through the enclosure with the compass on it. Maybe that isn’t as big of an issue as I think it is. But that’s my concern, anyway.
So as a work around, I was going to see if there was a way to simply replace the standard Pixhawk arming switch with a larger one.
Alternatively, I could have the emergency stop switch run a relay as @aamadeuss suggested. I’m not opposed to this method either, but it is a little more complex. It does solve both issues though.
Another option would be to put the emergency stop switch on the “power” box on the back of the rover, but it is less accessible there. It would be very close to the on off toggle switch on the rover at that point, kind of defeating the purpose of using an emergency stop switch in the first place.
Thanks for all of the feedback, I do appreciate it. It’s very helpful, as I’ve been stuck pondering this for a few days now and haven’t found a good answer.