The process is to get the tax return to properly reflect the return as originally filed. THEN you do the magic button to start the 1040X. If you scroll down you will see the figures for AS ORIGINALLY REPORTED and that is what you are saying has been calculated as a negative. If that is so, you need to go to those lines and enter the correct amounts.

Contact Support EITHER https://proconnect.intuit.com/community/proconnect-tax-news-updates/discussion/proconnect-tax-assist... OR https://proconnect.intuit.com/support/en-us/help-article/intuit-account-settings/contact-proconnect-... if this does not help you solve the issue.