Thanks for the visit and the kind words. :)
For something like this, it depends on how you best structure your thinking. Examples:
If it is easier for you to find your notes if they are represented like they are in an online binder, then set up your Evernote either as it is, and use a Notes tag for all notes. This tag will work across all Evernote (EN doesn’t allow duplicate tag names in the system) and can be filtered when you click on a notebook and then select the tag. Another possibility here is to have a unique tag per notebook, such as AL-notes in the Lit notebook. You could also change your notebook structure to have your subjects as main notebooks with each one having a sub-notebook called Notes.
If you want to stick closer to GTD methodology, you would simply set up your Reference notebook or tag as a filing cabinet that is organized alphabetically (by tag or even with sub-notebooks if it is better represented for you visually that way). You would then just file everything by alphabet and or number, though you could add additional tags here for subject or project if they are important to your being able to find the notes.
Ultimately, you need to consider two things:
1. What is the easiest way for you to get the notes into Evernote and get them organized without wasting time or breaking your brain trying to remember what tags and notebooks to use — when sending the items or during GTD processing.
2. What is the easiest way to find the information. If you are working on iPhone or iPad, for example, sub-notebooks are not currently supported, and neither is your organized tag groupings, so you will likely have to scan for the notebook or tag you want. Having clear tags will help here, and will make it easier for you if you decide to use the search functionality. Also, especially in the desktop version, saved searches could help you find information quickly. If you decide use the saved search functionality, it could change the way you view tags and notebooks.
With all that in mind, pull out the elements that you feel would fit most easily into the way you work and remember things.
I hope that was helpful! :)