Yes, the only thing you need to run RadControls for ASP.NET AJAX are the two assemblies - Telerik.Web.UI and Telerik.Charting. The new RadControls don't need a "RadControls" folder and they do not look for such folder.
Please try adding two DatePickers on an empty page to see whether everything looks as expected and afterwards, please try removing some of your application's CSS files to research where the problem comes from.
If you still have troubles, please send us a URL or a sample project, so that we can help you out.
the Telerik team