You're not actually doing an Amended return, are you? You don't amend a return if you haven't filed the original one. So you might need to undo the amended return and just finish the original return.
If you need to delete a payment, see this Extension FAQ for how to get there. Then you can change to amount to zero.
https://ttlc.intuit.com/community/tax-payments/help/how-do-i-get-credit-for-tax-payments-i-made-with...
