You can use Yii::app()->request->getBrowser() to retrieve the browser information. Based on them you could register an additional clientscript by using Yii::app()->clientscript->registerCssFile()
If that ie6 specific css will be applied to every page then the best place to put it would be in your layout file, clientScript won’t add the piece of markup for targetting IE so you should echo it out and use CHtml to echo it out.