You can place customized PHP configuration directives in the file /home/conf/php.ini. This file will not exist by default, so you'll have to create it and make sure it is readable but not writable by the web server (644 permissions). These options will be parsed at the master level (above even PHP_INI_SYSTEM); you may use any directive supported by the version of PHP you are using, including those marked as "php.ini only." Your php.ini file is parsed in addition to, not in lieu of, the system php.ini file, so you only need your site-specific changes.
Note: The php.ini file is not parsed on every request. Changes may take a few minutes of idle time to take effect. (Which, if your site is never idle, may mean they never take effect.) If you want to help it along, you can place your site in maintenance mode or temporarily disable it for a minute or two to ensure that all running processes are killed. Use the phpinfo() function to review the running config and confirm that your changes have been processed.
upload_max_filesize = "20M"
display_errors = Off
log_errors = On
extension = "/home/protected/mycustomphpextension.so"
For more information about which PHP configuration directives are available at which level, see the official PHP documentation.