I was able to find an answer from another list since the SE8C instructions are horrid. They only quickly touch on singaling for switch indications and nothing else.
Paul on RR&Co was able to explain how you set up the up to 4 heads per ribbon cable. I just need to set up the signal as top HG/HY/HR , middle as LG/LM/LR, and lower as Reverse HG/HY/HR. Now I just need to define the logic in the software so that if a head is not displaying green or yellow that it displays red by default.