If you're changing the color of the theme by using the default theme color settings found in the ClassiPress admin dashboard, then this isn't a customization and you won't lose the color setting you've selected. If you've changed any theme code though, then that is a customization and you would lose those changes when updating.
The link provided in my previous post offers more specific information regarding making actual customizations, but if you're simply referring to choosing settings within the theme which aren't code changes, then they are not customizations. From what you're saying, it doesn't sound like you're referring to customizations at all, just configuration. Thanks.