State and local income taxes paid can be an itemized deduction (Schedule A) on your federal return.

The taxes paid in 2018 through your withholding would be included as a deduction.  However, the amount you are going to pay with your state return will not be deductible on this 2018 tax return.  You can only deduct taxes in the year they are paid - so the taxes paid with your return would be paid in 2019 on go on your 2019 return (the one filed next April).