Make sure your malpractice insurance is paid before following @Camp1040 advice.  You can't amend MFS to MFJ more than three years after the due date of the separate returns.  It's a paper return, so make sure you get to the Post Office before they close and get a receipt with mailing date. 

Both refunds should be shown on Line 18 of the Form 1040-X.  You can override that line.  You can override anything you want, it's a paper return.