I'm not sure what you mean by "1040 SE." We are talking about Schedule SE and Form 1040-ES.
There is no direct connection between self-employment tax (Schedule SE) and estimated tax (Form 1040-ES). You have to pay self-employment tax when you have self-employment income. Being self-employed, being in business for yourself, or being an independent contractor are different ways of saying the same thing. If you are self-employed, self-employment tax is added to the tax on your tax return. For someone who is self-employed, self-employment tax is the equivalent of the Social Security and Medicare taxes that are withheld from the pay of someone who is an employee. You also pay regular income tax on your self-employment income.
Most people who are self-employed pay estimated tax because no tax is withheld from their income from self-employment. If the amount of self-employment income is significant in relation to their other income, the income tax on the self-employment income plus the self-employment tax is likely to result in not paying enough tax during the year, and having too large a payment due on their tax return. Paying estimated tax makes up for not having tax withheld. Estimated tax can cover income tax, self-employment tax, and any other taxes that are included in the tax return at the end of the year. The amount of estimated tax that you have to pay depends on your total tax for the year, any tax that you have withheld if you have a job where you are an employee (you get a W-2), and other factors. Form 1040-ES includes worksheets to help calculate how much estimated tax you should pay each quarter.
On your tax return, any estimated tax that you paid is added to any tax that was withheld from wages or other income. The total tax that you paid (estimated tax plus withholding) is applied to your total tax for the year. The total tax includes income tax, self-employment tax, and possibly other taxes. If you paid more than your actual total tax, you get a refund of the excess. If you paid less than the total tax, you have to pay the difference with your tax return. Estimated tax is not treated separately for determining your refund or payment due.
