When installing a Zendesk app you're given the option of enabling role restrictions. By restricting the app to a specific set of roles, you're also restricting which agents you're actually billed for.
To turn role restrictions on, click on the cog at the bottom left-hand side of the screen and at the top on the left click on 'Manage' under apps. Then hover over the app in question and click on the cog like this:
From drop-down menu choose "Change settings"
Then under the "General Settings" tab at the bottom, check the "Enabled" box next to "Role Restrictions".
Now you can choose which roles the app is turned on for.
If you're planning on restricting apps to specific roles, you should also read this article.