Hey!
I do not really get your diagram, so I will try to explain what you can do with Antimatter.
There are basically three templates for Antimatter: default, blog and modular.
The default template you can add a single "article" or whatever you want within a single markdown file.
The blog template allows you to add as many articles as you want in order.
The modular template allows you to add several "modules" in the order you want on a single page. Check out more info here: Learn Grav: Modular pages
The structure you have looks to be more complicated then what Antimatter can handle out of the box without modifications. Since you do not have a lot of experience creating themes I would strongly suggest learning Gantry 5 plugin. Gantry 5 is a template generator with everything you want out of the box and unlimited possibilities with some experience with css.
Good luck and have fun!