If you are setting up custom PHP settings, the custom php.ini file will be required in a folder where the php scriptneeds to execute. Or you can place php.ini anywhere and have this directive in public_html/.htaccess suPHP_ConfigPath /home/username/public_html where username is your cpanel account username, and it will pick php.ini from the folder public_html.
Check also the following resources:
- My server uses suPHP so each website has it’s own php.ini file. My hosting company recommended adding the following to my .htaccess
- suPHP – Documentation – apache/CONFIG