Please note: Plugin handshaking is automatic with no configuration options.
iControlWP Plugin Handshaking is a measure to introduce much higher security into the communication between your WordPress sites, and the iControlWP servers.
At its most basic level it works by ensuring that the iControlWP plugin, that is installed on your WordPress sites, will call back home to iControlWP every time it is asked to perform an action.
This is an extra layer beyond the Key and PIN that the service uses to authenticate with your site and ensures that even if somehow your key and PIN were compromised, the plugin would never perform a task unless it was first confirmed and validated against the iControlWP servers.
For more information, see our blog post here that outlines this a bit further.
Note: This extra option is only available on WordPress sites that support this feature.