The Federal return is based off of what is reported in Box 1. TurboTax will push the income to the appropriate place on the return.
What you really will need to ensure is how the income reports on the New Jersey return. On the NJ return, you will see a screen titled About Your W-2 State Wage Information. Because of state programming requirements, TurboTax includes both income lines as part of the NJ income. The next screen is titled Let's Confirm Your Taxable State Wages from (Employer). Click on the NY box so that those reported wages are not included on New Jersey's return
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