Hi casino83,
sorry for the late answer, but i have a very exhausting project these days :(
This is the way i do, which does not mean, it is the right way :)
I always duplicate the default Admintemplate and make my custom template for the backend. For any override i use the template.css inside the admintemplate.
For any frontend override, i use the standard tempate.css in my template folder. Again, i would not recommend to change the css-file(s) of any extension.
kind regards