Perhaps the way New York State does the ultimate tax calculation is leading to confusion. New York calculates the initial tax more or less on the federal income amount (even though lines 1 though 31 ask for the New York State amounts).
Only after it has calculated the initial tax does it prorate the initial tax based on the ratio of NYS income to federal income (line 45) to end up with the real NYS tax on line 46.
I am not sure that I have answered your question, but that's because I see what you are asking but I don't know why there is any confusion - just follow the instructions on the form.
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