Check out Part 3 of my Connections 5.5 Small Deployment series of guides, which takes you through the process of applying CR1. It's a mostly straightforward process, but I did run into a couple of gotchas with the Cognos components.
The Cognos Wizard needs to be updated on both BI Server nodes and the Transformer nodes, and that order of operations there with respect to syncing nodes is critical to avoiding errors. There is also a particularly nasty bug in one of the underlying Cognos update scripts that causes a problem on the Transformer node since the JAVA_HOME variable isn't set by default there. I've included a simple workaround to that problem in the guide to help you avoid problems.
Also take a look at Part 1 and Part 2 if you haven't seen them already.