You will need to install the remote agent on both nodes of the Exchange Cluster. Your selections will be from the Virtual name of the cluster not the physical names of the nodes. You will just need to select the Information Store(s).
Have a look at http://www.backupexecfaq.com/articles/using/backing-up-veritas-cluster-server.html - it talks about Veritas Cluster Server but you should select the same for MSCS.
