Let’s review. As you now know, the two are related – and you can’t have one without the other.
In short, if you’re self employed use Schedule C to calculate deductions (if you’ll have more than $12,500). If not, use the standard deduction.
Make quarterly payments for the se tax, based on your best estimates. When you do the annual filing, use your net income earnings to see how much se tax you owe based on that figure. Using the totals from your quarterly payments, subtract what you’ve already paid. Make a payment for the remainder.