When you enter the information into your federal return, the information will flow to your NYS return. After the entry into your federal return, the amount paid for student loan interest adjusts your taxable income by the payment amount, which is limited to $2500.
After all adjustments are made, your federal return now has an adjusted gross income or AGI. This federal AGI amount (which includes student loan interest) becomes the starting taxable income amount for your New York State return.