Thanks for reading my article!
I’m not sure if I understand your question completely, but this is what I can offer you:
When you originally set the Noteshelf notebook to sync to Evernote, it will go to the Noteshelf notebook in Evernote by default. However, once it’s there, you can move it to whichever notebook you wish and it will continue to sync properly.
However if, like Penultimate, you want each note within the notebook to be a separate note in Evernote, I’m afraid this isn’t possible without manually sharing your selected pages to Evernote.
Hope this helps!