Found a good article over on Nathan's blog detailing how to patch with the WUA client, Windows 2008 server code.
Support came for W2008C in ConfigMgr SP1, but to patch it you'll need to setup the usual on the ConfigMgr side then run a vbcript on the W2008C server to initiate the patch install.
http://msdn.microsoft.com/en-us/library/aa387102(VS.85).aspx
Here's another ace link, from technet on supporting Windows 2008 with the ConfigMgr client
http://technet.microsoft.com/en-us/magazine/2008.11.managing.aspx
Read the complete post at http://wmug.co.uk/blogs/r0b/archive/2010/05/15/patching-windows-2008-server-core-with-configmgr.aspx