Add the following code to the .htaccess file within your account's public_html folder (if one does not already exist, create one):
<IfModule mod_suphp.c> suPHP_ConfigPath /home/USERNAME/PATH/TO/INI/ </IfModule>
(replacing '/home/USERNAME/PATH/TO/INI/' with the appropriate path to your custom php.ini file)
Properly configured example:
<IfModule mod_suphp.c> suPHP_ConfigPath /home/example/public_html/shop/ </IfModule>
In the above example, the custom php.ini file is located at:
and that php.ini file is now recursive which means it will effect all of the web accessible directories within the account and not just the directory it's located in.