You can easily customize a set of jquery packages by setting assetManager in the configuration of application components (usually config/web.php ), for example, if you want to use the jquery file in the web/js folder:
'assetManager' => [ 'bundles' => [ 'yii\web\JqueryAsset' => [ 'sourcePath' => null, 'basePath' => '@webroot', 'baseUrl' => '@web', 'js' => [ 'js/jquery.js', ] ], ], ],
More details: http://www.yiiframework.com/doc-2.0/guide-structure-assets.html#customizing-asset-bundles
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