There is no “right” way to do this in MVC; it is up to you.
There are several common ways to do this.
You can place jQuery built-in functions inside your views by placing them in script tags for example.
<script> $('a').click(function() { alert("Click"); } ); </script>
However, this is usually not recommended, as it simplifies JS management and reuse and inflates your HTML. You probably would have done this only if you had a real little piece of script and it didn't feel like creating a new file.
Alternatively, you can put your html in separate js files and include a link to them in your views, for example.
<script src="~/Scripts/mycusomtjquery.js"></script>
This is better since it allows you to reuse and not inflate your HTML, and the browser can cache it.
An even better option is to use the Bundling function in MVC 4 and use it. Put js in a separate file, register it as a kit and do it in your view
eg.
Create js in separate files and put your own code there.
Put it in App_Start \ BundleConfig.cs
bundles.Add(new ScriptBundle("~/bundles/mycustomjquery") .Include("~/Scripts/mycustomjquery.js") .Include("~/Scripts/myothercustomjquery.js"));
Add a call to render the package in your view
@Scripts.Render("~/bundles/mycustomjquery")
This will make your js a miniature and unified way that can be cached by the browser.
You can customize this. Choose how to assemble your js files, how many actual js files to display, etc.