While the PHP handler running in cPanel server is FastCGI, enabling custom php.ini for a user is being described here. If the PHP handler running in server is suPHP, then simply it is required to copy php.ini from its location to either in user’s home directory or in document root(/home/$user/public_html) and then change the owner ship. But in case of FastCGI, php.ini file should be copied over to cgi-bin folder and do the rest explained below.
♦ copy php.ini to cgi-bin folder
♦ In cgi-bin folder, create a file named as php.fcgi and put the following in this file:
♦ chmod php.fcgi to 755.
♦ Upload .htaccess under public_html, put the following:
AddHandler php5-fastcgi .php
Action php5-fastcgi /cgi-bin/php.fcgi
and you are done.