Thats classic OR(experience, problem_OfOtherPeople) :)
no, joke. I read out, that you have problems with software architecture. This might be a key word to get you starting. I can't help you much here, except of telling my experience/thinking. You can also do study SA. Obviously, its not as easy, as one might think - if even a whole study can be filled with that topic.
But also, I think that still not the thing you need. SA can be seen as a kind of build-up structure of software, flowcharts, representations of functions, etc... for example, for communication of all the people involved in writing that software.
I think, one who's job is to write software, and not to design it, already do a kind of structure and software architecture in his head, by thinking in functions, methods, classes and imports. Without even know UML or other descriptors. So, this lead me into thinking its all experience and eloquent-ness in speaking that language.
Structure of Code / Software also does come from the "language" itself. Do you use libs? Imports? Or, do you rather write the whole thing into one large source code file? What imports do you need, what needs to be packaged into retail?
So this way, you're pushed into "thinking" what code to place where and into what module. This also very often lead to the need of refactoring of the code. Even in the "middle of a function" do some refactoring of other functions ...
I would say thats the agile method ;)
You could look up coursera on that topic. I wouldn't buy books, as the internet has plenty on topic.