No, it's not an estimated payment. Anything extra you had withheld using form W-4 will be recorded on your W-2 in box 2.
It's important that "extra" on a W-4 only means more than the default W-4 calculation. All your withholding is recorded on your W-2 and you never enter the "extra" separately. Estimated payments are separate payments you made directly to the IRS on their web site or by mailing a check.
