You pay the $200 since your tax refund should already be factored into the calculation on the Form 1040-X,
If you are e-filing the 2024 federal amended return, you can pay the taxes owed by direct debit from your bank account.
If you are mailing the 2024 federal amended return, you can pay the taxes owed by including a check with the mailed return. Or you can go to the IRS payment website using Direct Pay and make sure you indicate it is for tax year 2024 and an amended tax return - https://www.irs.gov/payments