You would mail in your check with a payment voucher (1040X). Beware that all taxes owed must be paid by April 18th to avoid a penalty and interest. You should mail your tax payment by midnight of the tax deadline date. which is Monday the 18th.
You can also e-file your returns, then go on the IRS website to make your Federal payment for taxes owed. If you do use the IRS website, then choose to pay your taxes owed by check, that would get you through to e-file your return. Then you can go to the IRS website for payments.
https://www.irs.gov/payments
If you owe State taxes, you can check your State's website for their payment options.
