I cover that in my article about automating the combine/minify process in Visual Studio.
To answer your specific question, you can test the IsDebuggingEnabled flag to determine whether you're in debug or release mode and emit different script references accordingly. For example, this is from the article's example:
<% if (HttpContext.Current.IsDebuggingEnabled) { %>
<script type="text/javascript" src="js/01-jquery-1.3.2.debug.js"></script>
<script type="text/javascript" src="js/05-jquery-jtemplates.debug.js"></script>
<script type="text/javascript" src="js/10-default.debug.js"></script>
<% } else { %>
<script type="text/javascript" src="js/js-bundle.min.js"></script>
<% } %>