Microsoft has a whitepaper that details Mobile Device Management especially using the Configuration Manager with the Configuration Service Providers.

http://download.microsoft.com/download/4/1/c/41cede8e-0e2a-4172-a517-4a6c3722d75b/Mobile%20Device%20Management%20White%20Paper.doc

Pocket PC Adaptation Kit for Mobile Operators is another treasure trove of information.

Here is a section on configuring Pocket PC devices:

http://msdn.microsoft.com/library/default.asp?url=/library/en-us/amo_ppc/htm/creating_a_cab_provisioning_format_cpf_file_zvvq.asp?frame=true