Non-refundable credits apply only to income taxes due. Regardless of what you have withheld. So if your income taxes are 18K then you will use the entire 18K in one year. In the example you listed above it sounded like your tax bill was 13.5K so you would use 13.5 out of the credit and roll the remaining 4.5 forward into the next year.
Once your income tax bill is settled then you have any additional taxes that get tacked on. This includes self-employment tax and extra social security or medicare tax due. Then that is netted against your withholding and the refund is what remains.
@legoman629
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