How can I customize the Apache Main Configuration settings not available in WHM?
The main configuration file for Apache is build using templates and updated during rebuilds with settings that have been configured through the cPanel software. While the WHM interface "Apache Configuration >> Global Configuration" easily allows you to modify common global settings in your main Apache configuration file, this does not contain all settings for the service. In the event you need to customize a global setting not present in this interface, you would need to create a custom local template to alter what is built into the configuration file.
We outline the process of how to create and maintain a local template file in the following article. It is advised you read over the entire document before deciding if this is the correct solution for you. Any global settings not contained within a virtual host would be present in the EasyApache 4 main template file referenced in this documentation.
If you are looking to add a setting or modify a virtualhost, you may instead want to review the following article.