Designing your Application Structure
When designing your application structure there are a number of components we need to think about. This can be a very confusing process when you get to the nitty gritty, but there are a few things to bear in mind to simplify any gotcha's you may come across in the future.
The key components you will be looking at at this stage are:
Your application structure will, pretty much be defined from your design work. From understanding your logical (navigational) structure and Information Flow you will have a good understanding of how to architect your application.
A key decision to be made alongside this is where do you actually store your documents? There are a couple of options and the detail of your own implementation will define the answer. There is no right and wrong answer here, and like anything with SharePoint there are probably 30 different ways of organising your information.
This page goes into more detail on where to physically store and surface your information.