Amend married filing separately to Amend Married Jointly

Apparently TT did my taxes wrong. It appeared beneficial to file as married filing separately this year due to money that was withdrawn from an IRA last year.  However my State has now changed my return from $903 refund to $74 due (so I have to write the a check for $977).  TT apparently put the homestead tax credit on both of our refunds and maybe I should have seen it, but that is what I have TT for.  I don't understand any piece of this.  So do I have to re-file both or if I do one will that suffice?  And what is needed in order to change from married filing separately to married filing jointly.  Last question, do I have to re-file both Federal and State as filing jointly or just the State?  Or maybe that should be 'Should I' amend both?  Thanks.