Sorry for late response, it is better to post in the general discussions area under SC community. This area isnt as well followed, hence the late reply.
Currently the granularity layer for vCD backup and recovery is orgs or individual vApps. There is no option to backup entire vCD environment. You can certainly build a backup configuration which has all orgs and vApps in it but I would advise against this. The more you backup at once, the more complex the backup becomes and thus more prone to failure but that is just my opinion. I certainly recommend backing up smaller units.
It is also not possible to restore a vApp to another destination. SC focuses on backup and recovery and restores back to existing container (certainly in future this could be option, just not today). In addition there is limitation today that SC cant restore a deleted vApp or VM. So if you delete VM or vApp from container or move it, the old backups you have cant be restored. This is because we are not tracking the meta data in vCD, we are working on this for future release but just want to make sure you have all the info in order to make a proper decision
Hope this helps
Keith