Hi,
You set the watcher node to run synthetic transactions against your Skype for business environment. The SCOM agent on the watcher node reports the status of these transactions back to your SCOM environment.
The process is - Create your test users in AD - deploy your scom agent to your watcher node - Install the skype for business server core files - configure your test users on the watcher node - create the watcher node configuration. I've used the guide below
previously to help set them up.
http://lyncme.co.uk/scom/watching-your-skype-for-business-2015-with-watcher-nodes-part-1-installation-and-configuration/