You can create a new site by running the command, punch setup. Setup command accepts a destination directory path to create the site. It will create the directory if it doesn't already exist.
punch setup mysite
In the above example, site will be created in a directory named mysite relative to the current path. If you don't specify a path, new site will be created in the current path.
You can specify a boilerplate to use when creating the site. Boilerplates are bascially Punch site structures which can be used as a base for a new site. Punch will copy the structure of the given boilerplate to the new site. Path of the boilerplate can be specified as --template (or -t). You can download any of publicly available boilerplates or use one of your own.