When we release upgrades template files will change and you will have to reapply all your changes again (that's if you can remember where they all are). If you keep your changes in a separate Custom CSS file you'll have no issues upgrading.
I can also add less variables like
@menuBorder;
@menuDropBack:
coming from menu-dark.less
or
@topbackground:
@topbackground2:
coming from header-dark.less