Is there any tutorial like small book about beans and how it is structured? And some schema with all boxes, and all possible markups (names)?
That will be more easy to build structure of pages. And if user know how is Beans designed, how work, then will be lighter to organize custom code and files.
Good thing will be to build some front online builder to drag and drop everything to faster building everything and when the builder will be saved code will be put same way like that with manual in php and less files. Is that possible?
The documentation available at this stage is what is available on Beans official website.
Regarding the structure of the framework, it is explained in this article. I would sugget to open Beans Core files and get your head around how things load which will make it much easier for you to understand how do modify it. About the markup names, you can dynamically find them in your browser inspector, this reply will help you to understand how to do so
It is not on the roadmap to build a Visual Builder.