We install a special plugin on your SNO site that cannot be deactivated, which will give you a new admin tab in your site's dashboard. Here's where you'll make most of your customization choices, such as Navigation Header Image, App Header Mini Logo, Splash Screen, Color Scheme, Primary Color, and Accent Color.
NOTE: Be sure the images you upload are the proper aspect ratio / dimensions as outlined. Otherwise they won't look good in your app.