android.moparisthebest.org/source/docs/theming/_template.markdown

The key source directories are as follows:

source/
  _includes/    # Main layout partials
    custom/     # <- Customize head, navigation, footer, and sidebar here
    asides/     # Theme sidebar partials
    post/       # post metadata, sharing & comment partials
  _layouts/     # layouts for pages, posts & category archives

It's pretty likely you'll create pages and want to add them to the main navigation partial. In the latest (version 2.1) To do that

Beyond that, I don't expect there to be a great need to change the markup very much, since the HTML is flexible and semantic and most common customizations be taken care of with configuration.

If you study the layouts and partials, you'll see that there's a lot of conditional markup. Logic in the view is lamentable, but a necessary side effect of simple static site generation.