Where would I add customizations to Apache?
Customizations made directly to Apache's configuration file area overwritten when the "rebuildhttpdconf" script executes. As this is the case, we recommend Apache Includes to prevent your changes from being overwritten. Includes made from WHM which we have documentation on here:
When Apache's configuration is then rebuilt, and the service restarted, the changes made to your includes will be included with Apache without the need to write them directly to the configuration file.