I would recommend that you not embed it, but let DNN handle the registration/loading of the resource. Doing so will allow you to easily see references to the JS if you have CDF disabled in DNN, and mask the references and have the content minified with CDF enabled in DNN.
Here is how to reference the client resource manager in DNN.
override protected void OnInit(EventArgs e)
{
DotNetNuke.Framework.jQuery.RequestUIRegistration();
ClientResourceManager.RegisterScript(Parent.Page, "~/Resources/Shared/scripts/knockout.js");
ClientResourceManager.RegisterScript(Parent.Page, "~/desktopmodules/DnnChat/scripts/moment.min.js");
ClientResourceManager.RegisterScript(Parent.Page, "~/desktopmodules/DnnChat/scripts/DnnChat.js",150);
base.OnInit(e);
}
pulled from https://github.com/ChrisHammond/dnnCHAT/blob/master/View.ascx.cs