Create an app as a service, but limit the users that see it and the folders it can access

I want to create an application that runs as a service account but only looks at a specific folder and subfolders.   It looks like when we add the app into our box enterprise, it will be seen by all users.

Is there a way to limit the service so that when it is added, only a group of users has access to it, and it only has access to a limited set of folders?   We do want it to receive events when a normal user drops files into the folder so that the service can process the files without human interaction, which makes me think it should be an enterprise service.

Is this the right way to go about this?