After you file

There were changes, i'll be getting $146.00 less than my original amount. I have a copies of the 8962 I filled out & all other documents that I sent them for my own records, but they specifically stated in their letter "Do not respond with a form 1040X, Amended U.S. Individual Income Tax Return."

I was wondering if I screwed up by faxing them the information they requested instead of submitting it through TT. So I still need to login into my Turbo Tax account & select amend my return? Do I send the amended return I do on TT to the IRS electronically even though they've already received my fax?