I guess that the first section of my answer is probably not what you want to hear but keep reading. My answer will also show you a little further how I use Evernote for GTD.
I never had/have the situation where I put a next action into two "where-contexts". If it contains just a single action to get it done, its not a project. In this case it either has to be done in the Office, at a computer (in this case, it also can be done in the office, but not exclusively), on the phone, and so on...
If there is just that single action where I, for instance, wait for an answer, that note exclusively goes to my "Wating For" list. But honestly, my "Waiting For notes" mostly belong to a project.
Notes in my Projects notebook are not actionable. They simply including a rough plan (bullet points, if it's a small project) of what I need to do in order to get it done. The weekly review, at the latest, lets me create my next actions of my projects.
But here is a point that I did not mention in my previous post: To keep all notes together that belong to a project (next action notes, notes of reference material and the project note itself), I tag them. That's about the only tag that I currently use. I can't explain exactly why I need this. I simply feels better to me if I can pull a list of all notes related to a specific project. Especially if it is a big one.
The project tags are named the same way as the title of my project notes.
I have 6 key categories where my projects belong to. 5 categories belong to my job and nr. 6 is my "private" category. To avoid adding a second tag, just to categorize my projects, I use a category-code as a prefix in front of my project. E.g. "10 Project abc" belongs to category X, "11 Project abc" belongs to category Y., and so on... It became second nature to me to use this notation for all my projects as I create them (the notes and the tags). Means I create the note and copy/paste the note title into the tag line within the note in order to create the tag. I don't move those tags into, for instance, a header tag, called "Projects" or so. I simply keep them where they are. The few header/parent tags I use to organize my reference notebooks, include a .(dot) in front of the name, to keep them at the top of my loooong tag list.
Maybe, someday I skip taging my project related notes. But for now, it feels right to me.