Secure backup is the only way to backup the entire device, including keys and certificates. Therefore, it is desirable to run it on a regular basis.
You can easily do it with dpbuddy using its support for "do-action" command. Secure backup is simply one of the actions with a few additional parameters.
Here's how it could be expressed using Ant and dpbuddy. Note that we're using "local://" filesystem as a destination; in reality you probably want to use "ftp:" instead.
<target name="secure-backup" description="Backup the entire device">
<tstamp/>
<dp:action>
<SecureBackup>
<cert>test-cert</cert>
<destination>local://sbackup-${DSTAMP}</destination>
</SecureBackup>
</dp:action>
</target>