I worked two jobs during the year and each employer withheld social security taxes. I know I can get refund of overpayment that was withheld from me on schedule 3. But half of the tax is paid by the employer. That half was also overpaid. What happens with that? Do I get the refund for the employer's half? Does IRS automatically send refund to an employer? Which one? I would like to understand what happens.
Nothing. Each employer was required to pay into the system based on the employees in their employ. Doesn't matter whether they overpaid or not. Your employer - based on his payroll - did not. Fair or no, that cash goes into the general kitty.
I also have self-employment income. Do I need to pay employer-portion of the Social Security even though I know it is over the annual limit due to salaries from other employers?
No, TurboTax will only apply the Medicare portion of the Self-Employment tax on your SE income. You can look at Schedule SE to see the limitation applied; Line 8a will be larger than Line 7, so the SS portion will be skipped over on the form. And half of that tax is subtracted on Line 15 of Schedule 1 as an adjustment to income on Form 1040.
I also own an S-corp that pays me some small salary. Does the S-corp need to overpay its half of social security even though it knows that the annual limit is already exceeded by other employers?