Battery Relocation has begun....

Just wondering when you guys installed the battery cut off switch on your 94/95, and you wire the alternator directly to the battery side of the switch, what do you do with the two wires that the original alternator wire attached to and that went into the power distribution box under the hood.

Do you have to hook the two wires up to a possitive comming off the battery or just cap them off and leave them dead? I assume since they were connected to the pos alt cable that they would have to be routed to a possitive battery cable source now?

The one wire coming out of the box went to the OEM starter/battery cable so I will put power to that, but I'm not sure on the other two wires that connected to the alt wire comeing out of the box.