Regardless of the SharePoint upgrade method chosen, you simply run the Nintex Workflow 2013 installer on the SharePoint 2013 server. Like SharePoint 2013, Nintex Workflow 2013 only supports content database migrations; by moving the Nintex configuration database to the SharePoint 2013 server and then running the Nintex Workflow 2013 installation and pointing to the existing Nintex configuration database.
Full details of the migration process are defined in the upgrade guide located at
http://connect.nintex.com/files/folders/upgrading_from_nw2010_to_nw2013/entry26920.aspx