As long as the same wires are plugged into the same place, you're good. As long as the same wire is plugged into the same lead on both ends, it doesn't matter which one. I usually do the side with the writing on it to the negative (black) lead.
Previous: 1993 Prostar 205
Red 1998 Ski Nautique, PCM GT40, 310 hp, , Acme 4 blade, Perfect Pass SG/Zbox.
Be kind. Have fun.