Actually, you are quite right when it comes to header/footer. Here is some basic information on how each of the major HTML5 tags can/should be used (I suggest reading the full source linked at the bottom):
Tag Archives: header
HTML5 new tags / elements
New Elements in HTML5 The internet has changed a lot since HTML 4.01 became a standard in 1999.
Embed WordPress Outside WordPress
From time to time you need data from WordPress, but should not displayed in the system; they are necessary outside the installation. There are basically two options. Content can be quite easy provide via feed and processed or you gain access to the system. And that is basically very simple and is briefly described here.