You don't. That's just how you report it on your tax return. First, Your total tax is calculated on your income. Then the withholding is subtracted giving you a tax due or refund. You have to start with the total tax on income.
If you have withholding of 11,666 and owe another 9,000 on your tax return then the total tax on all your income must have been 20,666. You needed to have 18,600 withholding to cover 90% of the total tax to avoid a penalty. (20,666 x .90 = 18,600)
