This is not particularly relevant to the fact that your urlManager is enabled, but rather how you register your assets.
You can simply add js and css files to your Asset Bundle, for example. /frontend/assets/AppAssets.php and make sure your package is published in a layout file, for example. /frontend/views/layout/main.php .
You can also try:
$this->registerJsFile(Yii::$app->request->baseUrl.'/js/plugins/sparkline/jquery.sparkline.min.js');
Instead
$this->registerJsFile('js/plugins/sparkline/jquery.sparkline.min.js');
which is looking for a file relative to the url, so it does not work with urlManager enabled.
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