The main problem you will face is that your Exchange server is clustered.
Backup Exec for Windows Servers will function correctly with a clustered Exchange server, even when a fail over occurs. For this you do need the BE Remote Agent on both nodes, but BE itself does not need to be clustered. Once the Agent is on both cluster nodes, you will configure a backup job to backup the IS via the virtual server name. By using the virtual server name BE will not be concerned with which node actually owns the IS resource at the time of backup.
CPS, which is required for the "continuous protection", does not support any type of clustering. So when a fail over occurs CPS will have no understanding of how to react. What CPS will know is that the resource is no longer available and the job will begin "failing."
So "continuous protection" of a clustered Exchange server isn't supported but regular backup of a clustered Exchange server will work fine with just the BE Remote Agents on both nodes going through the virtual server name.