There is no real need to backup the Secondary as you can load the saved Primary SSdb on the Secondary using ../SS-Tools/SSdbload -il -r 20 <filename> from $SPECROOT/SS directory.
The Secondary SpectroSERVER database should not be different from the Primary due to the following reasons:
You should not do any discoveries or modeling from the Secondary SpectroSERVER
You should not do any NCM captures from the Secondary SpectroSERVER
If you want to backup the Secondary SpectroSERVER you will need to use scripting with the utility StartOnlineBackup which can be launched from either the Task Scheduler or the crontab for the host system.
Apart from this you might consider setting the backup directory for the onlinebackup feature to somewhere outside of the Spectrum install directory- If you do this you could use a third party backup utility to automatically backup this directory which would enable you to restore to the Secondary if the primary was completely.