I am syncing Notebook using Dropbox and simply edit the notes directly in the Dropbox folder on my laptop. I'm using a Mac so do this using Apple's default TextEdit app. You could do the same using Notepad on a Windows PC.
You don't need to duplicate anything.
If you set up Notebook to sync via Dropbox and have Dropbox installed on your Mac, then all of your notes in Notepad will sync into the Dropbox folder on your Mac. All you need to do is edit your notes in the Dropbox folder on your Mac. Any changes you make there will sync up to Dropbox and when you open Notebook on your iPhone or iPad the changes will sync down to your device. Does that make sense?
But I have an ever better solution than using TextEdit on the Mac to edit your notes. I just found an app for the Mac that looks just like Notepad and sync via Dropbox. It works perfectly. Here is the link. http://www.notebooksapp.com
When you open TextEdit on the Mac, it opens with a Finder window. It should open where you last left it, e.g. your Dropbox folder.
In the lower right hand corner of that Finder window is a button - New Document. Simply click that and create a new document. You might want to first change folder in the Finder window if you have multiple Folders in Notebook.
As for the Notebooks app I mentioned, once you have specified the Dropbox folder that's what it will display when it opens and then you just click File - New Note to create a new note.
I'm not sure why you are having that problem. If I create a text file on my Mac using TextEdit, allow it to sync up to Dropbox, and then sync Notebook on my iPhone, it works fine. Notebook adds that date field in the brackets. It doesn't have to be there to begin with.
The only thing I have noticed is that longer file names don't work initially. I haven't worked out what the limit is yet but for example, a file named 'This is my second test note.txt' wouldn't sync (Notebook throws an error) but shorter names sync just fine. Once Notebook has inserted the date field, it seems any length file name is OK.
But that aside, it's working for me.