Info - Customizer is still BETA.
All options work correctly(in frontend), but not everything is displayed correct yet in the preview. We work on it.
♦ For correct work the Customizer requires default administrator template(Isis) and minimal recommended screen width 1280 pixels.
♦ When you open customizer it always opens in preview frame your homepage, so if you have a few different styles on your site(for example one for homepage and another for inner pages) don't forget to navigate to the page for current style.
♦ When you change something in the template(layouts, elements etc) save template before to use customizer
♦ Sidebars - To change background color of sidebar A and sidebar B - style selected should be 'Boxed', or 'Shadows' but not any gradient.
♦ Use the icon full screen for better viewing(2nd icon top left)
If you have any questions, ask it here