Yes, the Federal Credit is based on the cost AFTER any utility rebates.
As you say, it is possible you may not be able to use the full South Carolina credit, or it may take many years to fully use it.
If you are a Resident of South Carolina in 2016 and/or 2017, you probably should have been filing a South Carolina tax return, regardless of what your employers were doing with your paycheck withholding.
