If you want to make changes to the design of a dwt file then just open it as you would any other page and make the changes using code/design view. When you save it will update the other pages linked to that template.
In order to use these features, you need to add metadata to your site.
Metadata is stored in special folders which are hidden by default.
This common design is the result of my basing all my pages on a template containing all the above elements (logo, navigation menu, 2 column layout, etc).
Using a template makes the job of adding new pages to much easier than it would otherwise have been: any time I want to add a new article, all I need to do is to use that custom template and insert my article content into the right column.
If you look at all the pages on using a desktop browser, you will probably have noticed that practically every page shares the same basic layout.