Yii::app()->clientScript->registerCoreScript('jquery');

You can use coreScriptPosition for this.

Directly from the docs:

Where the scripts registered using registerCoreScript or registerPackage will be inserted in the page. This can be one of the CClientScript::POS_* constants. Defaults to CClientScript::POS_HEAD.

Use like this:

$cs = Yii::app()->clientScript;
$cs->coreScriptPosition = CClientScript::POS_HEAD;
$cs->registerCoreScript('jquery');

Another useful link to read on this. (Read the comments too)

--Edit--

You can tell Yii where to put the script in the method:

Yii::app()->clientScript->registerScript(string $id, string $script, integer $position=NULL, array $htmlOptions=array ( ));

The $position variable will be the position of the script on your page.

And can be any of these:

• CClientScript::POS_HEAD : the script is inserted in the head section right before the title element.
• CClientScript::POS_BEGIN : the script is inserted at the beginning of the body section.
• CClientScript::POS_END : the script is inserted at the end of the body section.
• CClientScript::POS_LOAD : the script is inserted in the window.onload() function.
• CClientScript::POS_READY : the script is inserted in the jQuery's ready function.