When a patch deployment is performed, Security Controls records the machine name in the database if it does not already exist. From there, the number of remaining seats available for deployment is reduced by one for each target. If you elect to use Security Controls Agent, each agent machine is allocated a license and also counts against the total number of license seats available. If the same machine is managed in both an agentless and agent-based manner, that machine is counted only once.
You can easily find out how many license seats have been used by choosing Help > About Security Controls.