Wordpress Plugin Boilerplate (Structure of Plugin) - Custom Post Types, Meta Boxes and Saving Meta Info?

I just got a hang of writing my first plug-in. It consist of two custom post types, with two different types of custom meta boxes attached to them. I got the saving of that working and even a function for a shortcode and displaying it on the front end.

But it all turned out really messy, so I decided to rewrite it. I came over something called "WordPress Plugin Boilerplate" which did seem pretty popular. But I just can't understand where I should put everything.

http://ift.tt/1EN4kHZ

Could anyone explain to me where I should play for example, custom post type, add meta box, saving that meta box info etc.

IF NOT maybe someone has a good summary on good plugin structure?

via Chebli Mohamed