First, you will need to paper file the return; you can only e-file an amended return if you had e-filed the original return yourself using the same software program.

Go ahead and copy the original return, using the Override function so that Form 1040 is filled out exactly as the original return was.  You then go ahead and open up Form 1040-X.  At that point, when you make any further changes, the changes will be reflected on the 1040-X form, which provides the basis for the amended return.