Quarterly estimated taxes are paid in to the IRS throughout the year to cover the tax on your self-employment income. Here's a link to the Form 1040-ES, which has a worksheet for calculating how much tax to pay.
https://www.irs.gov/pub/irs-pdf/f1040es.pdf
The amount of income you use in the calculation for the self employment income is the actual profit, not the total earnings. Your goal is to make sure that you do not end up owing $1,000 or more at the end of the year when you file your tax return. There are some additional stipulations with estimated tax penalties that you can find here:
https://www.irs.gov/pub/irs-pdf/i2210.pdf
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