Tax return amendment

Using Turbotax, I've filed how much I need to pay back to IRS and scheduled my payment on April 1st. However, during reviewing, I found my mistake and mailed my amendment to request some payment back using Turbotax. I am still waiting for IRS's confirmation regarding this amendment. On April 1st, should I pay the money I filed first and get the amended return later? Or should I pay the difference between the submitted payment and the amended return?