I couldn't create a project from scratch either. What I did was use phalcon developer tools to initialize a project.
Maybe this can help you to check structure; https://github.com/phalcon/mvc
And you can find more examples: https://github.com/phalcon/awesome-phalcon and https://github.com/phalcon
Is necessary you know at least some php knowledge and preferably, at least you should know how other frameworks work to get an idea because phalcon is somewhat difficult (indeed the documentation is sometimes very general but in this forum some examples published can help) but as you understand you notice that it is more flexible and if you need to modify or implement new features is easier than others.