Please Note: To backup a single file in excess of 5GB, a Backup Vault would be required
SQL Server Backup Recommendations
For SQL Server, you can use regular backup mechanisms to get an archivable copy saved to a folder on a local disk or file share, then point the block backup job to that folder. If you do not want to keep local copies, you can just configure the SQL Server backup plan to always use the same filename (overwriting what's there), and rely on JD for managing previous versions.
See also the following articles on creating SQL Server backups:
Exchange Backup Recommendations
The following article from Microsoft provides general guidance on Exchange backup:
When following the above guidance in conjunction with Jungle Disk, you can choose "Normal" or "Incremental" to create a backup to a local disk or file server, then use JD to copy those archives to the cloud. If doing a "Normal" backup, you can use the same filename each time (overwriting the previous local backup) and let block backup take care of handling previous versions (i.e., snapshots).
An alternative is to use the pre- and post-scripting support to shutdown Exchange, run a backup directly on the Exchange data files, then restart Exchange. However, for a mission-critical mail server this really isn't a great approach, especially for the initial backup which can leave your server offline for hours.