Do you compartmentalize the disks again, or do you just make different folders?

Yes, when you are not using BTRFS. Due to OMV using ext4 as default you basically create your Raid and then folders/networkshares on top of it.

ZFS on the other hand allows you to create datasets which are separate ZFS filesystem object that can have its own settings (quota, reservations, permissions, etc.). The “same” goes for BTRFS which supports BTRFS subvolumes.

I do not know how well OMV supports BTRFS and how well it is integrated in the overall workflow. Therefor I cannot give a recommendation if it is feasible to use BTRFS on OMV.