When selecting your Virtual Machines, Add Objects, change the view to VMs and Templates, drop down your vCenter, and your Folders appear. Select whichever folder that contains your VM's that you want. From there, down to your Guest Processing; Applications, Edit, there's no way to exclude individual VMs' processing from your folder. Credentials; it appears to apply to the Folder; cannot also exclude or choose different credentials for VM's of said folder here either.
I realize you can if you choose individual VM's for your source rather than folder, but this omission pretty much kills the purpose and use of folders if we can't take that route.
Veeam B&R v9
Dell TL2000 via PE430 (SAS)