You just need to understand the concept of partials in the Stacks plugin.
You may group any collection of stacks inside a 1 column stack, say a navigation bar stack for example. Hit the partial button at the top of the stacks window (see image), and now that creates a partial stack in your stacks library.
You add that stack to any page you want in your site.
Now when you are editing any page of your site, you can double click the partial that is sitting in the page, and it allows you to edit the contents. Anything you change will be reflected in every instance of that partial you have deployed on all the pages in your site.
You can partial any stacks. So you can make your own theme nav, footer, whatever, and it will be consistent everywhere you place it.