You can wait to amend until the first amendment is processed. If you owe money with the second amended return, then you will incur a penalty and interest until the taxes owed are paid in full.
If you want to wait to amend your return for the second time, you can pay any amount you owe on the IRS website for payments.
https://www.irs.gov/payments
If your Federal amended returns affects your State return, you would need to also amend your State return. If you owe taxes on your State return, you can pay on your State's website.
