First of all, I think that not exist one way to do it. My organization in Evernote is a constant work in progress. Before telling you how I do it, I think you should write down an structure of notebooks and tags, and try link them as you can, and then find out which is the best way for you. Notebooks and tags are Free.
I have a typical GTD structure, but I make some little changes that don't go against with the GTD method. For example, In my GTD, I have actions, projects and PROJECTS. Yeah Yeah Yeah, I understand the difference between " wash my teeth" ( one action ) , and " go to the doctor " make the phone call reservation, have the date, go to the doctor. ( more than one action, it's a Project ). But " get Married" , is not the same as going to the doctor. So that's a PROJECT. So inside my Project Notebook, I a Have Project Get married. And what's more, that project has a tag. Just in case I have some information that is related to the PROJECT but is not specifically of that project.
In my life when a project Finishes I review if I want to keep something, and the delete Everything. The idea is getting things done, and find quickly related information, not being a librarian .
Use the tags you want the times you want, the same for project notebooks. GTD is like customizing your second brain. I bet your " brain operating system" will always have an update once. If you need more information about how I specifically structure my mind, I think that you will learn somethings, but your Mind I think. I have copied others structures for months, and never worked at all. I recommend that you should use Evernote as a second brain. And the main difference between EN and your physical brain, is that scanning the EN is much more easier. You can see your thoughts organized, and that give you the chance to improve your organization. The final light probably you find that less is more, and you learn how to focus in a new way.
Sorry for my English!