One more way to organize directories for applications with front-end and back-end.

// This config contains common settings for other config files.
 
return array(
    'basePath'=>dirname(__FILE__).DIRECTORY_SEPARATOR.'..',
    'name'=>'My Web Application',
 
    'sourceLanguage'=>'ru',
    'language'=>'ru',
 
    // preloading 'log' component
    'preload'=>array('log'),
 
    // autoloading model and component classes
    'import'=>array(
        'application.models.*',
        'application.components.*',
    ),
 
    'modules'=>array(
        'News',
    ),
 
    // application components
    'components'=>array(
 
        'db'=>array(
            'connectionString'  =>  'mysql:host=localhost;dbname=mydb',
            'username'          =>  'root',
            'password'          =>  '',
            'charset'           =>  'utf8',
        ),
 
        'errorHandler'=>array(
            // use 'site/error' action to display errors
            'errorAction'=>'site/error',
        ),
 
        'log'=>array(
            'class'=>'CLogRouter',
            'routes'=>array(
                array(
                    'class'=>'CFileLogRoute',
                    'levels'=>'error, warning',
                ),
            ),
        ),
    ),
);

return CMap::mergeArray(
    require(dirname(__FILE__).'/base.php'),
    array(    
        'components'=>array(
 
            'urlManager'=>array(
                'urlFormat'=>'path',
                'showScriptName'=>false,
                'urlSuffix'=>'',
                'rules'=>array(
                    // News.
                    'news'=>'News/newsReport/list',
                    'news/<id:\d+>'=>'News/newsReport/show',
                ),
            ),
        ),
    )
);

return CMap::mergeArray(
    require(dirname(__FILE__).'/base.php'),
    array(
        'components'=>array(
 
            'user'=>array(
                'loginUrl'=>array('site/login'),
                // enable cookie-based authentication
                'allowAutoLogin'=>true,
            ),
        ),
    )
);

class WebApplicationEndBehavior extends CBehavior
{
    // Web application end's name.
    private $_endName;
 
    // Getter.
    // Allows to get the current end name in this way: Yii::app()->endName;
    public function getEndName()
    {
        return $this->_endName;
    }
 
    // Run application's end.
    public function runEnd($name)
    {
        $this->_endName = $name; // Set end's name.
 
        // Attach the changeModulePaths event handler and raise it.
        $this->onModuleCreate = array($this, 'changeModulePaths');
        $this->onModuleCreate(new CEvent($this->owner));
 
        $this->owner->run(); // Run application.
    }
 
    // This event should be raised when CWebApplication or CWebModule instances are being initialized.
    public function onModuleCreate($event)
    {
        $this->raiseEvent('onModuleCreate', $event);
    }
 
    // onModuleCreate event handler.
    // A sender must have controllerPath and viewPath properties.
    protected function changeModulePaths($event)
    {
        $event->sender->controllerPath .= DIRECTORY_SEPARATOR.$this->_endName;
        $event->sender->viewPath .= DIRECTORY_SEPARATOR.$this->_endName;
    }
}

'behaviors'=>array(
    'runEnd'=>array(
        'class'=>'application.components.WebApplicationEndBehavior',
    ),
),

protected function init()
{
    // ...    
 
    // Depending on the value of Yii::app()->endName we can configure our module in different ways.
    $this->newsPerPage = (Yii::app()->endName == 'front') ? 5 : 15;
 
    // Raise onModuleCreate event.
    Yii::app()->onModuleCreate(new CEvent($this));
}

class BackEndController extends CController
{
    public function filters()
    {
        return array(
            'accessControl',
        );
    }
 
    public function accessRules()
    {
        return array(
            array('allow',
                'users'=>array('*'),
                'actions'=>array('login'),
            ),
            array('allow',
                'users'=>array('@'),
            ),
            array('deny',
                'users'=>array('*'),
            ),
        );
    }
}

define('YII_DEBUG', true);
 
$config = './protected/config/frontend.php';
require_once '../yii/framework/yii.php';
Yii::createWebApplication($config)->runEnd('front');

define('YII_DEBUG', true);
 
$config = './protected/config/backend.php';
require_once '../yii/framework/yii.php';
Yii::createWebApplication($config)->runEnd('back');