Steve,
The Brown and Yellow wires from the throttle switch are connected to the two wires from the brake levers (Blue and Red on mine) which go to the blue connector. This allows the brake levers to cut the power as normal, but it also means that the throttle switch can also cut the power (and apply regen too).
Unfortunately my pie is one of the early ones which were not programmable, so I have the factory preset level of regen, which is very effective on a 25.9V pack, but less effective when using a 51.8V pack.
Alan