Quarterly estimated tax payments are not just for your business. Since your business is a pass-through entity, your business income is not taxed separately from your W-2 income or other personal income. On your tax return, basically, all of your income is added together and the tax is calculated on the total. The tax withheld from your paychecks as an employee, and your estimated tax payments, are added together and applied to your total tax. That's why you can choose to increase the withholding on your W-2 income to cover part or all of the tax on your business income, or make larger estimated tax payments to cover part of the tax on your W-2 income. It's only the totals that matter.
