OK, i know this is a huge gap from last reply on this thread, but here goes anyway,
I have also set up the same 2-1 cyclops head on my printer (CTC dual, sailfin 7.7 firware), and now am facing the same issue.
Wiring is not an issue and i have that sorted, my issue is i know nothing about firmware but want to have it setup so the toolhead offsets are set as needed to allow 1 nozzle............
My question is did you get the offsets sorted? and if so how?
Thanks, p.s your machine looks awesome