I am using the 'Automatic Generator' of GitHub Pages, and I see it only generates a single index.html and other web resources.
How it works if I want to have a multi-page website generated from other markdown files?
You pull the generated page, make any modification and addition you like (including adding new pages and links between the pages), then commit and push.
The generated single page helps you to make you start. You can duplicate its layout to generate other similar-looking pages by hand.
See Help.