Actually what you should do is take all the customizations you've made thus far and put them in the custom.css.
To explain, the way the theme is structured the CSS is split into style.css (which holds the base), minimal-skin.css (which holds the light color scheme), dark-skin.css (which holds dark color scheme), shortcodes.css (which holds the CSS for the shortcodes), and custom.css (which overrides the default settings from the other stylesheets).
Now when Kriesi updates a theme he may make changes to the stylesheets. The only one he never touches though is the custom.css. So for example, if you deleted the minimal-skin.css or say made changes to style.css when you updated the theme your customizations would be lost and minimal-skin.css would be added back to the folder.
Also like you experienced with the social icons each stylesheet serves a purpose. The minimal-skin and dark-skin stylesheets gives the theme its colors or images for social media icons, bullets, dividers, etc. So in the end you may have less headaches by activating minimal-skin.css (like you've already done) then just copying it's content into custom.css and working from there. Reason why I suggest that is in doing so you'll already have the correct styles you need in order to change font color, header background, etc.