Loading two CSS files

I've just upgraded to v4.0, and I'm using a custom theme, which I set using the admin page. My custom theme works fine, but when I viewed the source, it shows that it's loading the simplemenu.css and themes/custom/custom.css file. All my styles are in the simplemenu.css and not in the custom.css file. Is there a way to prevent it from loading the custom.css file, which doesn't exist? Or, since I'm using a new version, should I move my style information into a custom.css file, and if this is the case, what styles are to be in the main simplemenu.css?