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You can pay yourself a bonus at the end of the year and elect to withhold almost all (you still have to withhold your share of FICA and Medicare taxes) of the bonus withheld in federal income taxes. Withholding is treated as being paid in four equal installments when an estimated tax penalty is calculating, so even though you were underpaid in the beginning of the year, withholding at the end of the year will catch you up on your payments.
Going forward, if you still do not want to take more wages, the only other way ensure you are fully paid in is to make estimated tax payments. However, since it sounds like you have not been making estimated payments, the only other way to catch up is through bonus withholding.
Any estimated tax penalty an also be reduced by annualizing your income. This method requires you to complete Form 2210 and calculate your federal income tax liability based upon your actual income, deductions, and credits for each quarter, so if you tax liability is skewed toward the end of the year, the estimated tax penalty will be reduced if not eliminated.
I hope this answers your question. Please let me know if I can clarify anything or answer any additional questions, and I would greatly appreciate positive feedback. Thanks, Jonathan