I don't think there is an out-of-the-box way to have a user in the directory so they can control their device, yet not show up in the corporate directory.
Using the latest IP Phone Services SDK, you can create your own Corporate Directory XML script that does not list users without a telephone number value in the directory, so you could do that.
The Manager field is used primarily in conjunction with ART at this point, so a manager can login to ART and see the call records for the employees that report to him/her.