You need at least three conventions:
- find a way two refer to refer to the paper notebook
- find a way to refer to the particular entries in the paper noteboook
- find a program in the computer, in which to store the reference
As I review the contents of the notebooks over the years (some of them go back to the late eighties), I might decide to transcribe some of the entries into ConnectedText, putting a link into the content page for the notebook and putting a cancellation mark in the paper notebook itself. Not everything is deemed important enough for transcription, though this changes over time and many things end up in my ConnectedText over time. I have a category called "My paper notebooks."
Reviewing them (both the paper and the electronic) notes often is an important part of what I would call my "work flow," if I did not despise this phrase. I could, of course, use a digital camera for the transcription step, but I find transcription makes me remember the note better.
I recently came across a post in which a more fine-grained approach is suggested, namely that of keeping an index in every notebook: "The back of your notebook will act like a tag list or index. Every time you create a new entry at the front of the book you're going to 'tag' it." If you follow this approach, you could later transfer the index into your electronic note-taking application at your leisure. The marks on the pages would allow you to locate the information you look for quickly.
As I said, it is a more more fine-grained approach than including a Table of Contents in the notebook. I am not sure I need such a level of detail in accounting for my paper notes (because anything I deem really significant gets transcribed anyway), but others may find the approach described here more useful. Also, remember that most books have both a Table of Contents and an Index. So, you could do both, if you find it necessary or useful.