suPHP does not support the php_value/php_admin_value directive known by mod_php to parse configuration options to scripts for certain virtual hosts or directories. All the php_flags in your .htaccess will have to be moved to php.ini, which you will have to create in your public_html directory.
Example:
.htaccess php_flag register_globals on
php.ini register_globals=on
You will have to move every command on .htaccess that starts with php_flag.