sign in looks at the "blank.html"
drag and drop on the main page "customize" looks at the dndindex.html
the site uses the general.html
In most cases you won't edit the master pages. You will just add custom css in the admin panel. It really all depends on what you are trying to achieve. You can start by looking at the docs on theme customization. Use inspect element to find css elements you are wanting to try to adjust. If you are not familiar with css, there is plenty of info on the web to help. The master pages contain html, and php along with some script that functions with the core.