When determining under withholding penalty, the IRS does not make a distinction between the amounts that are withheld on a W-2 vs the amounts that are made in separate estimated payments.
You can adjust your W-2 withholding any time mid-year by submitting an updated W-4 to your employer.
In order to avoid owing an under-withholding penalty, you must meet, at a minimum, ONE of the safe harbor provisions below:
1) You owe the IRS $1000 or less when you file your taxes.
2) If your AGI in the prior year was less than (150,000 joint / 75,000 single), you had at least 90% of the tax you owe for the current year withheld.
3) If your AGI in the prior year was less than (150,000 joint / 75,000 single), you had at least 100% of the tax you owed for the prior year withheld.
4) If your AGI in the prior year was more than (150,000 joint / 75,000 single), you had at least 90% of the tax you owe for the current year withheld.
5) If your AGI in the prior year was more than (150,000 joint / 75,000 single), you had at least 110% of the tax you owed for the prior year withheld.
Also note that estimated tax payments are supposed to be paid quarterly, in proportion to the amount of income earned in that quarter. There is a whole worksheet that deals with that. I've never found the IRS to bother me about small variations, but that's just my experience.
Also, I'm not an accountant, tax advisor, nor attorney, so seek out your own advice from a pro.
In my opinion, the most conservative, fool-proof method to meet safe-harbor is #5 -- Simply withhold more than 110% of what your entire federal tax burden was for the prior year -- and do it by cranking up your W-2/W-4 withholding if possible, in order to avoid having to worry about your quarterly payments being "spread out correctly."