I am sure that others will chime in, but here are the three ways that I have dealt with it in the past:
1) If I had more withheld than I paid in tax the previous year, I didn't worry about it,
2) If I was SURE that I would have more than 90% of my tax liability for the year withheld, I didn't worry about it,
3) I adjusted withholding to cover what was needed. Even if you do this the last pay period of the year for thousands of dollars, the IRS will pretend that you had it withheld over the course of the year.
I believe that each of these three will avoid the penalty for underpayment. Of course, quarterly tax payments will do that, too.
I am not a tax attorney, blah, blah, blah...