Turbotax may pick up any extension payments done through the app but nothing paid directly or outside of the app. if they were as you go through the amended returns you must enter these payments. Exclude any underpayment penalty that you paid with the original return
.Turbotax should be showing the original balance due. why it isn't is unknown. hopefully you kept a PDF or printout of the original. you need to check every line in column A to make sure it matches the original. Otherwise you should be able to get a tax return transcript using the iRS website.
https://www.irs.gov/individuals/get-transcript
