Whatever "extra" amount you are having the employer take out for federal tax per week will still end up in box 2 of your W-2, so you should enter your W-2 exactly as it appears and enter the amounts exactly as they look in the boxes as supplied by the employer. There is not a "special" box on your W-2 for the "extra" withholding.
And box 17 will show the state tax withheld.