If you set up for direct debit when you efiled the amended return then all you can do is wait ... when the return eventually gets processed the debit should happen. This could take more than 6 months to happen AFTER the original return has fully processed.
It takes about four months in normal times. This is not a normal year. The IRS is far behind. They were still processing million of 2019 returns before 2020 tax season started.
Did you submit the amend after your original return was fully processed? I am surprised that they did not deduct your payment. Give the IRS a call and see if someone can update you on what is going on.
This get me through the fastest IRS Phone Number | Call Now & Skip the Wait (gethuman.com)