SCOM monitoring clusters

The MP Guide for the Cluster MP will help you through this process, but a few of steps you definitely need to take are:-

Install an agent on each physical cluster node

Enable ‘agent proxy’ for the agent on each physical cluster node. This will allow the physical nodes to submit discovery data for the virtual cluster resources….including the virtual cluster server, which will ultimately appear as ‘agentlessly’ monitored

Disable Windows Event Log replication between the cluster nodes. This is enabled by default and will likely result in duplicate events being reported from the physical nodes.

Just a few thoughts, but have a good look at the MP Guide for assistance.
AGENTLESS MONITORING-A brief explanation

One of the things that falls into agentless monitoring in SCOM is Clustering. When you install a scom agent on the physical cluster nodes, those agents monitor the virtual cluster resources running on top of those in agentless mode.
Therefore the agentless monitored machine refers to the virtual cluster server name for a cluster i.e. an agent has been  installed on each physical cluster node and the virtual cluster server appears as ‘agentlessly’ monitored.

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