I would remove backupbuddy and just not use it at all. You don’t need it. You can create a cron job for different types of backups, whether database, your files, etc.
To list current cron jobs on your server, the command is crontab -l and set up a new cron job, its crontab -e.
Setting up a cron job is easy, what you need to learn is the times you need it to run. It would look something like this:
MIN HOUR DOM MON DOW /bin/sh command > /dev/null 2 > & 1
* * * * * /bin/sh command > /dev/null 2 > & 1