"how to put these numbers in schedule c where should I put the payroll taxes"

Yes, we covered this before. There is no such thing as Payroll Tax for the person or that business. You will change everything that seems related to payroll, to be Draw = owner Took the funds. That is not business expense. You remove it from Expense. There is no Salary, no FICA, no SUTA and no FUTA. Any amounts treated as payroll are no longer Payroll.

And waiting on the IRS to respond to the 941-X means you are simply waiting for them to refund the amount, which you would then give to him, or he can put into the business bank account as part of owner funds (like returning a draw or as if that is new money invested), because a Schedule C business is not tracking Retained Earnings or Stock Shares for the business in the tax filing.

"but he paid over 2000 in payroll taxes."

Which is what you should have requested be refunded, by filing 1 or more 941-X (per quarter that the wrong 941 was filed).

You don't need to wait on the 941-X. You need to have all of the business info from 2020 finalized, and the personal data, too, if you are preparing the 1040. The 941-X is not part of any of this.

Fix the data, then use it to file taxes. I would not file for an extension unless there is something you don't have and you know you are expecting, such as something in their personal tax picture hasn't come in, yet.

And yes, this person needs guidance for filing "quarterly estimates" if that applies, because the first quarter for 2021 is due April 15. Then, June 15, Sept 15 and Jan 15, 2022 (roughly).

That means he needs to be prepared to pay what he owes for 2020 and the first estimates for 2021. His State might have a similar requirement.