if you didn't file you can input these under Deductions & Credits / Estimates and Other Taxes Paid, it's not automatic, though some people have been complaining this topic doesn't come up in the interview flow.
if you already filed, what was the outcome - did you have less refund on your return, or have to pay more to the IRS then realize later it was wrong? I think in this case you can just wait and see what IRS does to your return, they have a record of your ES payments and independently check for mistakes like this and recalculate underpayment penalties etc.
