CRM provides a way for updating clients using its own update manager however this requires your users to have admin rights on there computers. This situation is far from ideal so I have found a way to publish CRM 4.0 hotfixes using SCCM and SCUP. This guide will take you through the steps to get CRM hotfixes available for deployment via SCCM. It assumes that you already have SCUP installed and configured to look at the same WSUS server that SCCM is using. It also does not cover the process of deploying the hotfixes from SCCM when they appear in the list.
SCUP
Adding "Trusted Publishers" certificate with Group Policy
Recently having installed SCUP and set it up to publish updates using an internal CA I needed to deploy the custom certificate to all the client machines so that they will receive and install the updates correctly.