Without question, the best way to customize files in a WordPress theme is with a child theme. That way you’ll have an easier time updating the parent theme when an update is released.
To help you create a child theme, we’ve written a series of posts on the Organized Themes Blog that you can use as a guide. Here are links to the posts:
- Child Themes For The Win (http://www.organizedthemes.com/creating-a-child-theme/)
- Doing More With Child Themes (http://www.organizedthemes.com/child-themes/)
- Advanced Child Theme Usage (http://www.organizedthemes.com/advanced-child-theme-usage/)
If you have any questions about creating a child theme, feel free to post your question in the forum for the parent theme.