Currently customizing your open data website using the site configuration UI is not enjoyable. Using the wizards for basic customization is relatively easy, but using your own code is not due to the UI setup. Having three different windows (header, body, and footer) that are unable to be expanded makes it difficult to understand and see the full scope of the HTML in your final website configuration. It is also confusing when trying to understand which div elements are required and not able to be deleted or changed and where those div elements are located within the entire webpage's HTML due to the breakdown of the header, body, and footer portions of the site configuration. Further it makes it is difficult to properly create and organize your custom HTML when certain elements are not visible in the "code" windows.
My suggestion would be to have a possible third option for configuring your open data website. I would extend the ability for a user code their own webpage by allowing them to upload an HTML page to be used in the site configuration. Possibly giving the user an initial template with the default and required HTML elements to start their site configuration from.