There are two sets of data that can be backed up on your WholesaleBackup Server: the server's meta-data, and the user data. The meta-data includes all the data necessary to recover and reestablish your WholesaleBackup Server in case you have a computer failure and need to reinstall your server. The user data is all of the data and meta-data generated by your backup accounts, and is what is required to do restores for each particular account.
Backing up Meta-Data
All critical meta-data for the WholesaleBackup Server is backed up automatically. To configure the frequency and destination for this particular backup please visit the Settings->Local tab (as documented here). For obvious reasons you should specify a folder on a network share or separate disk to backup these files.
Backing up User Data
There is no automatic backup of the user data folders. You can find the location of each customer's data on the Dashboard->Accounts tab in the ‘Folder’ field, as shown here. The initial default location for that data was specified as the "New accounts in folder" field on the Settings->Local tab, as documented here.
Once located, you can use any tool that replicates data between locations to back up the user data. Programs that provide rsync-like functionality, as well as automatic scheduling are useful for this, as they allow you to do incremental syncs as well as set the time you sync your user data. Similar to backing up your meta-data, you should do the backups of your user data to a network share or other offsite location.