You can still add them as you normally would. Here's a very simple example.
WebUserControl.ascx
<%@ Control
Language="C#"
AutoEventWireup="true"
CodeFile="HomePastAttendance.ascx.cs"
Inherits="UserControl_Print"
%>
<link rel="stylesheet" href="http://code.jquery.com/ui/1.10.2/themes/smoothness/jquery-ui.css"
/>
<script src="../Scripts/jquery-1.4.1.js" type="text/javascript"></script>
<script src="http://code.jquery.com/jquery-latest.js" type="text/javascript"></script>
<script src="Scripts/JScript-local-file.js" type="text/javascript"></script>
<script src="//ajax.googleapis.com/ajax/libs/jquery/1.8.3/jquery.min.js"
type="text/javascript"></script>
<script src="http://code.jquery.com/jquery-1.9.1.js"></script>
<script src="http://code.jquery.com/ui/1.10.2/jquery-ui.js"></script>
<script src="Scripts/JScript-local-file.js" type="text/javascript"></script>
<script>
$(document).ready(function () {
$("#datepicker").datepicker();
});
</script>
<%@ Register
src="PagerControl.ascx"
tagname="PagerControl"
tagprefix="uc1"
%>
<style type="text/css">
.style1
{
width: 100%;
}
</style>
<h1>Print past attendance:</h1>
<p>Start Date: <input type="text" id="datepicker" /></p>
<br />