Do you have a cluster defined in vCenter? Do you have shared storage?
Generally speaking, you want to capture/collect metrics from all consumers of resources belonging to VMs you wish to monitor. For example, you want to monitor VM A. VM A resides on host A. Host A also hosts VM B and VM C. In this case you want to monitor VMs A,B,C entirely since you want to capture all of the workload that is running upon the resources of VM A. This applies to host systems, datastores, etc. This is because if you do not capture all consumers of the resources, you're going to have blind-spots in your capacity planning and analysis. This is bad. So typically we say, the most narrow collect we want to see is the cluster or datacenter level. Really, though, it depends on how shared the resources are between the resources you wish to monitor. If, let's say, you have a datastore shared between 10 clusters... and VMs are running on that datastore across all 10 clusters.. ideally you'd want to collect/monitor/license all of the VMs upon that datastore to ensure you don't have any blind spots.
On the licensing subset config - you need to be mindful of the perms to VMs at the VM & Templates view in addition to the Hosts & Clusters view.. vCOps can get at the VMs via both the security hierarchy paths and it'll utilize the most 'permitting' security to get it's information.