I'm pretty new to angularJS myself, but from what you described, if the changes are purely CSS,
when the user selects to apply a theme instead of another, I'd simply add a CSS class to the body element,
and then have my CSS account for it.
In other words, I'd have CSS for these two:
#MainContent { background-color: white; }
.alternateTheme #MainContent { background-color: black; }
When the user clicks on the button to activate alternate theme, I'd grab the body tag and add the alternateTheme class to it
HTH,
F.