Create new page for subfolder

On the first page of the control panel a user can click add and create a new page with a specified template. How do I store this created pages in a sub folder?

Unless you specify a parent page for subpages in your pages section, the parent will always be the current context, so in site.yml, the page will be created as child of $site.

So that means to create subpages for different pages, you need a pages section for each parent.