I have been experimenting with my Neo Smartpen and syncing with Evernote. Here is what I have found.
Once you establish the Neo Notes/Evernote sync, an EN notebook will be created called "Neo notes".
In the Neo Notes app, you have only 1 master active notebook. If you create new notebooks in Neo Notes app (I create a new notebook for each client), and then sync, these notebooks will populate in the Evernote Neo Notes stack (but they will be empty). All Neo Notes will be in your "master" notebook, but in Evernote you can drag-n-drop a note from your master into one of the other Neo Notebooks (my client notebook). Once you do this, then each time you update that specific page in your physical Neo Notes notebook (then sync), the updates will be in your Evernote notebook.
Each new notes page created will only appear in your master notebook, so you'll have to drag-n-drop them into the respective Evernote Neo Notes notebook.
Sorry if this is confusing, but it does help to combine both my Neo Notes and specific EN in the same notebook.