The idea behind the project structure is to have the code for your application separate from the framework code. To achieve this, Philly is just a dependency for your application. Dependencies get managed via composer, so Philly is a composer dependency (see here on packagist.org).
ricardoboss/Philly is the PHP framework which contains the building blocks for your application.
ricardoboss/PhillyFramework is a template for applications, which use the Philly framework.
To create an application using Philly, please continue with the Installation.