If you haven't set a user's manager when you first added them to the system, or if you need to change their manager, you can do so through 'Configure > Manage users'. Select 'Manage all users' and click on the employee's name to take you to their profile. Click 'Edit profile' to update their details - you can also change their Team or Department here.
If you have enabled the option in your account settings, employees can select their own manager by clicking on 'Profile' in the left-hand menu or 'Your profile' in the right-hand drop-down menu. To enable or disable this ability head to 'Configure > Account settings > Profile settings'.