When installing a Zendesk app you're given the option of enabling role and group restrictions. By restricting access to the app, you're also restricting which agents you're actually billed for.
To turn restrictions on, click on the cog on the left 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 the drop-down menu choose "Change settings"
Then under the "General Settings" tab at the bottom, check the "Enabled" box next either "Role Restrictions" or "Group restrictions".
Now you can choose which roles the app is turned on for.
If you select multiple roles (and no groups), the agent only needs to be in one of the roles to have access.
If you select multiple groups (and no roles), the agent only needs to be in one of the groups to have access.
IMPORTANT: If you enable both group and role restrictions, the agent must be in both one of the roles listed and one of the groups listed to have access.
If you're planning on restricting apps, you should also read this article.