You can amend a Married Filing Joint (MFJ) return to a Married Filing Separate (MFS) return and vice versa. When amending a MFJ return to a MFS return, first delete all information associated with the spouse on that return. This includes all Form W-2s, Schedule Cs, Schedule SEs, etc. Anything that can be denoted as 'spouse' needs to be removed. Next, change the filing status to MFS.
NOTE: Once you have filed your tax return as Married Filing Joint (MFJ), you CANNOT amend your filing status after the April 15th deadline. Any change to filing status has to be done before the deadline.
When changing from MFS to MFJ, select the taxpayer you'd like to be the primary taxpayer. Change the filing status to MFJ, then add all information pertaining to the other spouse.
NOTE: Once you've filed your tax return as Married Filing Separate (MFS), you have three years from the original deadline to make the change to your tax return. This deadline DOES NOT include any filing extensions.