i think that adding your scripts to a custom folder in your scripts folder is the way to go.
you can create a new bundle in the appstart\BundleConfig.cs file as follows:
bundles.Add(new ScriptBundle("~/bundles/custom").Include(
"~/Scripts/Custom/myCustom.js",
"~/Scripts/Custom/myCustom2.js"));
and than add the bundle to your view like this:
@section scripts{
@Scripts.Render("~/bundles/custom")
}
this will be rendered at the @RenderSection("scripts", required: false) line on your layout file.
OR
To call only one specific script for your view you can do:
@section scripts{
<script src="~/Scripts/Custom/myCustom.js"></script>
}
note: you can drag the script file from the solution explorer into the section. you don't have to write the entire path.
EDIT - seems important so i copied this from my last comment:
in order to use minification you need to add your script to the bundle table and either add BundleTable.EnableOptimizations = true; to the BundleConfig file or set <compilation debug="false" in your web.config file.