They are totally separate.
You report your business income and expenses on schedule C and calculate your net income. That flows to schedule SE and you will pay 15% self-employment tax on the business profit (the equivalent of social security and medicare withholding from an employer).
Your net business income also flows to your main form 1040 where it is combined with all your other income (wages, investments, gambling, etc.). Then you subtract either the standard deduction or itemized deductions, depending on your situation. You calculate your taxable income and your income tax, and then apply any tax credits (dependents, electric vehicles, energy efficient home improvements, etc.) to find your total income tax.
As the last step, your income tax and self-employment tax are combined. Then you compare your tax to your payments and withholding, and you either get a refund or owe an additional payment.
