We use to actually use that folder configuration but moved everything to the public directory and use .htaccess to hide those folders now because of the need to have the assets folders bundled with each module. If you are really needing to do that, there are a few paths you may need to change. The first would be to create a folder to contain all the asset folders for each module. For example, you could create a fuel_assets folder right next to the assets folder at the web root. Then create subfolder for each module and put the assets folders in that. Then you'll need to change the $config['assets_module_path'] in the application/config/asset.php file to something like this
$config['assets_module_path'] = 'fuel_assets/{module}/assets/';
The second path you'll need to change is the INSTALL_ROOT constant at the top from:
define('INSTALL_ROOT', str_replace('\\', '/', realpath(dirname(__FILE__))).'/fuel/');
TO
define('INSTALL_ROOT', str_replace('\\', '/', realpath(dirname(__FILE__))).'/../fuel/');