Eilon wrote two very helpful forum posts on the recent changes in UpdatePanel.
What's up with UpdatePanels and how come nothing works? http://forums.asp.net/thread/1440058.aspx
HOWTO: Write controls compatible with UpdatePanel without linking to the ASP.NET AJAX DLL http://forums.asp.net/thread/1445844.aspx
This second article goes in depth on how to use the new registration APIs on ScriptManager, but without linking to the Atlas assembly.