You can add your own logo and change the banner in your store to show your school colors.
To do this, go to Online Store Module > Store Settings
Within Store Settings > Store Theme you can select the color you want to appear on the left side banner of your store as well as choosing to use the logo uploaded into your site.
The organization logo can be uploaded into your Site Settings > Organization Logo
Once you have uploaded the logo and changed the color of your preference. You can view your live store to see how it looks by clicking View Store