You can cover it any way that you wish, either with extra wage withholding or Form 1040-ES. The IRS does not care how you do it as long as you cover what you owe, and there's nothing special to file with your return for a single 1040-ES payment, aside from remembering the payment of course!
Personally I lean heavily on the 100% prior year liability safe harbor rule. If there was a large surge in income not subject to withholding (an unexpectedly large dividend payout or capital gain situation) I give my tax situation a close look in early December and compare what will be withheld to the prior year's liability. In most years I've been covered but for one year I did need to run up to payroll and tell them to withhold an extra $500 in taxes each week and then reverse it on the last day of the year. (Left the payroll weenies scratching their heads, but they complied.)
I've had a couple of great years in the past where I generated an extra 5-figure tax liability which I paid on April 15th, without a dime in penalty due to the safe harbor provisions. In fact, I generated an extra $5,000 in taxable income in 2006 on the 2005 TAX that sat in my investment account from Jan 1st to April 15th. Needless to say, that was a pretty big tax check (biggest personal check I've ever written) and an unusually good rate of return for those few months.