You need to go ahead and send your payment. The IRS will not review your amendment until they have completed processing your tax return. According to the IRS, they want amendments to be mailed after they finalize
your original return and you receive your refund or your payment has processed.
Amendments can take up to 14 weeks to be completed by the IRS. Then you will receive a refund for the overpayment of taxes paid.
The
following IRS link is very helpful in understanding the amendment process:
https://www.irs.gov/newsroom/amending-your-tax-return-ten-tips