Updating WordPress would possibly overwrite any changes you make to your files also I believe. Then you would have to remember where to re-add that code. This could be a bad idea if you're running with several plugins and start changing files by hand. I'm not speaking as a professional but I believe it would be best if any changes to files should be left inside the templates of a Child Theme References: http://codex.wordpress.org/Child_Themes http://codex.wordpress.org/Theme_Development