Jay-Cee, I do not know. Do you have brake handles with switches built in? If not, then there is nothing to connect the brake input of the controller to, and I would just leave it alone.
If you do have brake switches or one switch, and it has two wires, then it's easy. Connect the two wires from the switch to the two wires to the controller. If it's only one wire, then you have to find out what your brake switch does (maybe it connects the one wire to ground when you brake?), and what the new controller expects for it's input. Maybe pulling the yellow wire to ground is what it needs. But I do not know that.