To change the HTML structure or PHP output of some files you must create a copy of the file in the child theme and make your changes there.
Therefore, if you wanted an example this is what you would do: 1.) I want to change header-one.php so I go and copy the code from the file in the main theme. 2.) Create the templates directory in the child theme if it isn't there already, then create a header-one.php in the templates directory. 3.) Then open the new empty file and paste the code into the file. 4.) Make your changes to the HTML or PHP of header-one.php, and then perform the same steps if you update the theme in the future.