Can I update or do I need a child theme?

Hey there, I'm the web editor of Atrium Magazine. You can find our website here. We have Photofocus Pro, which is available for an update. However, when I go to update it notes that "any customizations you have made to theme files will be lost." We've made several customizations through a plugin called 'Custom CSS and JS.' Do those count as customizations to the theme file? I want to update, but I don't want to lose our customizations.