mojoPortal content management system is designed to produce flexible markup that allows you to have a good deal of control over the design and semantics. Our flexible container panels can be configured from the theme.skin file and give a great deal of control over the rendered markup, there are also settings for individual features like the Blog that allow you to configure a lot of properties from theme.skin to control the layout and markup in the Blog.
Basically, the outer skeleton of markup comes from the layout.master file where you have almost complete control over the markup, then there are the pockets where features are rendered along with feature specific content from the database. The features generally use a set of container panels and headings that can be configured from theme.skin and then inside those is where content from the database is rendered. The content from the database is exactly what you enter in the WYSIWYG editor (ie what you see in the html view of the editor is exactly what is stored in the database. So, these 3 levels, (the skeleton from layout.master, the configurable panels and headings, and the content entered directly in the database) combine to give you a great deal of control over what gets rendered while also providing some default markup configuration that provides the hooks to make a consistent design from CSS.
As of version 126.96.36.199 we are providing some reference skins to help you get started with HTML 5 design in mojoPortal. Our Framework skin that is included with mojoPortal is built using the Bootstrap CSS framework. If you haven't heard of Twitter Bootstrap, it is a popular HTML 5 CSS Framework that provides grid systems for layout and some other common design elements. Some aspects of Framework are already pre-configured to illustrate the use of HTML 5 structural elements like header, article, aside, and nav. You may need to adjust it to suit your personal needs, or for the specific structure of your site to enhance SEO. Note that the Framework skin is not very pretty, it is intended as a starting point for a new skin development, but over time we hope to have additional designers participating in this project and adding new html 5 skins with a bit more visual character.