If you have an amended return pending in the system it does affect your eligibility for the monthly CTC payments, so you will end up waiting for the CTC as a part of the refund you get on your 2021 tax return instead. You will not get the monthly payments.
Even during “normal” times it takes about four months for the IRS to process an amended return. During the pandemic and due to the severe backlog at the IRS it is taking much longer—six months or more for many amended returns. Do not expect quick results from amending. When the IRS issues a refund for an amended return it will be by check. They do not make direct deposits for refunds for amended returns. You can watch for information here:
https://www.irs.gov/Filing/Individuals/Amended-Returns-(Form-1040-X)/Wheres-My-Amended-Return-1