How to override php.ini:
1. If you allow user to override php.ini, then edit /home/user/public_html/.htacces :

suPHP_ConfigPath /home/user

Or if you don’t want user freely edit their php.ini file, then add these directive in virtual host configuration /etc/apache2/sites-enabled/:

<VirtualHost *:80>

…………………

IfModule mod_suphp.c
suPHP_ConfigPath /home/perpus
</IfModule>
</VirtualHost>

2. Copy /etc/php5/cgi/php.ini into /home/user/php.ini, then edit accordingly. Warning, if you just create a new php.ini and add a few options in it, then the other options (max upload, disabled function, etc) will be resetted in to default php configuration. So, it will be better if you copy from the main php configuration.