You should never amend a return until your original return has been accepted and fully processed. The original return and amended return are processed separately from each other. An amended return can take over 6 months to be processed.
You can check on the status of your Amended return on the IRS website Where's My Amended return. Once that is processed, the IRS (& State) will see you paid the amount on your original return.
https://www.irs.gov/filing/wheres-my-amended-return
If you are still having problems you would need to contact the IRS (and your State if amended a State return), to have them help with your amended return.
IRS Toll-Free Help
You may call 800-829-1040 with any Federal tax questions. Don't select you are asking about a refund, because it will just send you to the automated system for refunds.
