It is highly recommended not to change the System module. In fact, in 2.5 the System module will be read only.
You have two options:
In both cases you can define additional attributes in the new metaobject.
It is indeed not recommended to change the system module; leave it as it is.
What you will probably need to do is create a new Object (for instance 'Employee') and let this new object inherit from System.User.
This will give the 'Employee' the same characteristics as System.User, more information on Inheritance and how it should be used can be found here: Wiki Inheritance