With some more help from Technet (http://technet.microsoft.com/en-us/library/hh847255.aspx) I found the following seems to work:
Add-ClusterCheckpoint -ResourceName "SQL Backup Agent-<INSTANCE>" -RegistryCheckpoint "SOFTWARE\Red Gate\SQL Backup\BackupSettings\<INSTANCE>"
Add-ClusterCheckpoint -ResourceName "SQL Backup Agent-<INSTANCE>" -RegistryCheckpoint "SOFTWARE\Red Gate\SQL Backup\BackupSettingsGlobal\<INSTANCE>"
Thanks,
Geir W
Add-ClusterCheckpoint -ResourceName "SQL Backup Agent-<INSTANCE>" -RegistryCheckpoint "SOFTWARE\Red Gate\SQL Backup\BackupSettings\<INSTANCE>"
Add-ClusterCheckpoint -ResourceName "SQL Backup Agent-<INSTANCE>" -RegistryCheckpoint "SOFTWARE\Red Gate\SQL Backup\BackupSettingsGlobal\<INSTANCE>"
Thanks,
Geir W