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After you file
@PatinWA Fanfare is correct. The return that has to be amended is your return. You already put your SSN on that return. Your spouse cannot prepare a joint return using your SSN, because it will be rejected.
When you amend:
When you enter your own information in My Info, you have to answer the question "Were you married?" If you click the button for Married, then a drop down will appear that asks, "Do you want to file this return together with your spouse?" Then you choose yes to file a joint return. You would then enter your spouse's information into My Info. Whenever you are entering income information there should then be a spot for you and for your spouse's income information. Income screens will have spots with each spouse’s name—be careful to enter under the correct names.
Your spouse will not file a return at all. All of her information goes on the Form 1040X that you prepare and file as a joint return.