this is simple steps to Prevents users from overriding system php.ini in suPHP mode .... in CPanel servers

first : you must make sure that suphp is installed as default handler
than just edit your httpd.conf file or php.conf file ( will be better to use php.conf )

now add this line :
suPHP_ConfigPath /usr/local/lib
or ( Zend )

suPHP_ConfigPath /usr/local/Zend
if you need to use only php.ini config file :

suPHP_Config /usr/local/lib/php.ini
goodluck ,,