I want to know how can I add an asset only for IE9 in yii2 assets bundle? I mean like
<!--[if lt IE 9]>
<script src="assets/js/html5shiv.js"></script>
<script src="assets/js/respond.min.js"></script>
<![endif]-->
and another thing is how can add a js library like jquery in top of page not in the end?
You have to specify the options for your jsOptions property.
In your case, it should be something like:
public $jsOptions = ['condition' => 'lte IE9'];
Further reading: http://www.yiiframework.com/doc-2.0/yii-web-assetbundle.html#$jsOptions-detail and http://www.yiiframework.com/doc-2.0/guide-structure-assets.html#asset-options
Regarding to the jQuery question, you just configure the AssetBundle's accordingly, or you can just register it in your head or wherever you want in the template inserting the normal script tag.