If your talking about an LM-2S (not likely), then the other four wires on the 6 pin harness are outputs 5 and 6 (Green and Violet) and inputs 1 and 2 (White and Yellow).
If your talking about an LM-3S, then the other four wires on the 6 pin harness are outputs 5 and 6 (Green and Violet), an input (White) and a negative (Yellow).
How to wire up the number boards on an Athearn Genesis or Scaletrains is heavily dependent on how your wiring up the model in the first place. Are you taking out the factory motherboard(s) and hardwiring the LM in or are you using a 21 to 9 pin adapter harness?