Where should I add customizations to Apache?
Customizations made directly to Apache's configuration file are overwritten when the rebuildhttpdconf script executes. We instead recommend the use of Apache includes to prevent your changes from being overwritten. We have documentation here on includes made via WHM:
When Apache's configuration is rebuilt, and the service restarted, the changes made to your includes will be included with Apache without the need to write them directly into the configuration file.