With the many different types of php modes, this means the method of adding custom per-domain changes can vary greatly.
Check your custombuild options.conf to determine which php1_mode you're using, and find the related guide below.
mod_php is the default and the most commonly used. You can use 3 different methods to change php settings:
.htaccess in the public_html to add php_admin_flag / php_admin_value
php-fpm is handy for multiple instances of php, allowing the User to change php version from within their User Level area. php-fpm does not support .htaccess changes as php-fpm is it's own stand-alone php server, but you can use
and the call to fastcgi will read that in if it exists. Note that it's a full replacement and not an 'addon' ini, so ensure you have *all* settings you need in that file, as the default php.ini isn't used here. Take a look inside the User's httpd.conf to see which .sh script is called, and the variables passed. Then check inside that .sh script for more info on how it works.
Note that some settings like disable_functions can only be set once in the main php.ini file, and cannot be overridden by other areas, but this varies per php-mode. php-modes like php-fpm/fastcgi are much more stand-alone php instances, so you can get away with these types of overrides, away from the main php.ini.