How do you set it up for a Win2k server? Unless I've missed something the policies are applied to the client, not the server, and those policies can be stored in policy files which reside on the server and pointed to by the client. In this case it doesn't matter if the server is Win2k or Samba, the client wouldn't know the difference.
I certainly could be missing something but that is the way I used to do it. If I am missing something it would help me greatly to get a detailed example of how you currently apply policies to your clients.