Ok, so McCormack is resigning and the Governor is going to appoint a replacement, so that is going to lead to a special election. The question is how do I separate that from the judicial incumbent who is staying on the court and wont have a special election?

You add the one who's staying to the special election as an incumbent and give them no votes but a win. They will show as a "Holdover".

Thank you, so when the governor makes an appointment, just classify it as a special election and put the incumbent in, plus the new appointee the incumbent gets 0 and the new one gets 1 vote and just mark both as winning. Just want to make sure I get this one right when it happens in a few weeks

That seems correct. Though I think you can classify it as an Appointment.