Alternater wiring

I swapped a dauntless 350 in to my 70 and at the alternater theres a "bat" terminal which I attached the 2 red leads in the commando harness. I'm left with 2 smaller leads (black/brown??) each with a eyelet in the commando harness and the typical chevy style 2 lead (red/black) plastic plug on the alternater. Memory tells me the one red lead on the alternater gets 12v when running, anyway, can I run the harness leads into the alt leads? Anybody done it? It's not fully running yet to check voltage. Thanks.