If you are writing a complex model, while it is ultimately math, it has more in common with the skills required to write a great essay than it does with the skills required to do complex calculus. A great essay is understandable on multiple levels of detail: if you read just the introduction you should get a sense of what is going to happen in the essay. If you want a more detailed explanation of what exactly happens it should be contained in a logical place later on in the essay. The body paragraphs should reference the structure of the introduction and they should contain those arguments in more detail. If you are writing a particularly large body of writing you might need a more expansive structure: chapters, maybe even multiple volumes etc.

The same should be true of your application. If I read the main file of it I should get a basic idea of what is going to happen. If I want more detail I should be able to understand clearly where to look for the detail I want.