Here are some options:
1. Mail in your payment with a payment voucher: https://www.irs.gov/pub/irs-pdf/f1040v.pdf
2. You can pay your taxes due online with the IRS: https://www.irs.gov/payments
3. You can set up an installment agreement and then when the amended return is accepted call the IRS and work with them updating your payment plan: https://www.irs.gov/payments
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