It doesn't look like I can set a backup repo when creating a job using Add-VBRBackupJob. You can only set a folder path, which creates a new backup repo. I am assuming it can be changed after the job is created by using Set-VBRJobOptions. The help for Add-VBRBackupJob reads that the -folder parameter is not required but it seems that it is required.
An issue I see is that I need to set some type of junk path when creating the job which in turn creates a junk repo. Is there a way to set backup repo when creating the job? I just started playing around with v6. I may just be confused on how to properly use a backup repo.
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In the future I would like to see an Entities property (like Add-VBRJobObject) for Add-VBRBackupJob. Since Veeam can backup VMs from multiple vCenter servers the possibility arises that you could have multiple VMs with the same name. If I am creating a job via powershell and adding a VM via its name (string) and that VM's name is duplicated in more than one environment Veeam will put all VMs with that name into that newly created job.
I think all of this is already possible, but I'm still ramping up on V6 PowerShell.
The Add-VBRBackupJob cmdlet is really deprecated in V6, you should be using the hypervisor specific versions of these command, Add-VBRViBackupJob (vSphere) or Add-VBRHvBackupJob (Hyper-V). These cmdlets require a "Repository" object, which can be populated by the Get-VBRBackupRepository cmdlet. Also, these new cmdlets support adding VMs by Entity, so that addresses your other concern as well.