You don't have to change anything if you don't want to. The Administration module is just added to Mendix projects for your convenience, so you always have a way to create user accounts without first having to create forms and/or microflows for this purpose.
When you already have some form of user administration in your project (sounds like you have, as you stated you've got Employee entities inheriting from System.User and I'm assuming you also have some way to create/edit these objects including their username/password and permissions), you could just delete the entire Administration module (or only keep the parts that are still useful to you).