To make your account in cpanel  server have custom php.ini for all subfolder                       You need to use below code steps

1)   Login to server via SSH

2) scp /usr/local/lib/php.ini  /home/cpanelusername/public_html/

3)   vi /home/cpanelusername/public_html/.htaccess

Add below code

suPHP_ConfigPath /home/pankaj12/public_html
<Files php.ini>
order allow,deny
deny from all
</Files>

Once done custom php.ini should be available for all accounts