That's not a great situation to have, in that you can't tell vC Ops which to apply a license to. If you can split up the monitoring at a cluster-level, that would be ideal, e.g. 25 VMs in one cluster (licensed for vC Ops), the rest in other clusters. Splitting up the monitoring any other way (e.g. monitoring only 'some' VMs in cluster) would give you a split monitoring scenario, which is not the greatest situation to have since it gives you blinds spots int he infrastructure. Basically you see hosts, clusters, and data stores utilizing resources, but you only "see" a subset of the workload (VMs) consuming the resources.
You limit vC Ops's pervue of moitoring using vCenter perms on the vC Ops collection account. You can 'no access' the account at the VM & Templates levels as well as Hosts and Clusters level to block vC Ops from grabbing stats on the VMs.
vC Ops counts 'powered on VMs' against the license count and updates that count every 20-30min.
See the following KB on split/subset monitoring: