Dude, I just had the same concern. Thankfully, IRS did electronically debit the taxes due on my original return, which makes me think that the turbotax email asking to make the payment by check as some kind of glitch in the system.
Furthermore, I also checked the current status of my amended return following this link (https://www.irs.gov/filing/wheres-my-amended-return), and found the same to be in progress.
FWIW, it's always better to keep a tab on your IRS account (https://www.irs.gov/payments/view-your-tax-account) ,as that's the ultimate source of truth.
