Your custom theme and its associated files will be contained in the sites/all/themes folder with the name of your theme (mytheme). Never change files outside of your theme directory as these changes will not be migrated to production.
For more information on theming, view the Drupal 7 theming guide for specifics.
Subtheming from a YaleSites theme
In addition, any of the YaleSites themes (Yale Standard, Yale Boxed, Yale Wide) can be used as a starter theme and duplicated. This provides a good starting point for your custom theme. The YaleSites themes use the Omega base theme, a flexible interface that provides all the regions necessary to build a dynamic site and follows the typeface standards set by the University Printer. See YaleSites Starter Documentation for more information.
Creating Layouts with Delta and Context
Creating your custom theme requires advanced technical skills. Please consult the drupal.org documentation, support options or User Groups to find a solution. If you have found a bug please file a bug report. Or even better, provide a patch file to fix the problem. If there is a module you need, please request it on the YaleSites Forum. All requests will be considered providing they do not create redundancy with functionality that already exists.
Important notes on creating a custom theme
Be sure to rename your theme to a descriptive name that matches your site.
Do not add SQL to your theme to build dynamic content. Themes are for display only. Use the Views module instead to create lists of content.
Hiding your theme from other sites
Since every YaleSite is derived from the same code base, your theme sits alongside other custom themes for other sites. Read more about hiding your theme from other sites.