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You always and only file one tax return listing all your income. Your self-employment income goes on schedule C along with your business expenses. The net profit (income) flows to schedule SE to calculate your self-employment tax and it flows to form 1040 to be combined with your other income, deductions and credits to calculate your overall income tax owed. Your tax liability is your income tax plus self-employment tax. If you paid more into the system than you owe, you will get a refund, otherwise, you owe an additional payment.
If you don't want to pay estimated tax payments, you can adjust your withholding so that more money is taken out of your paychecks to cover the tax from your self-employment income. The IRS just wants their money on time, they don't care how you pay.
However, be aware that the tax system is pay-as-you-go. You may owe a penalty if you underpay during the year, even if you get caught up in full when you file your return. You will owe at least 30% tax on your business income (net after expenses) and possibly more depending on your tax bracket. If you don't have enough tax withheld from your job to cover the taxes from the job plus 30% of your net self-employment income, you may owe an underpayment penalty at the end of the year.
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