skb, If you really like pen and paper then try to approach it both realistically and methodically.
First: Work out your expectations? (Not hopes, nothing so vague and often deluded, but what you can realistically expect of yourself, knowing who you are and how you work.)
Second: See how you can streamline the mechanics of achieving those expectations.
I suggest that you give up the idea of directly transcribing notes into your computer; that's
not (in my opinion) a good use your time and resources. Instead, concentrate on the best features of each (paper vs computer) and try to merge them.
For example:
Label your notebooks - I generally use a date range printed on the front, but you may find it simpler just to number them. Also work out whether you can be bothered numbering the pages (it can help for what I'm about to suggest, but it's not essential, or you might split it into marked quarters as it's easy enough to use a pen to mark the outer edges of the notebook pages so that the quarters are visible, almost like tabs). Now, on your computer you set up one or more files as indexes into your notebooks. You might have a simple text file like this:
Code:
Book# Section Subject Keywords
25 Q2 Zombies on the 'net Comedy, Gory
25 Q3 Vampires of the Sahara Movie-script
Or you might create a database or spreadsheet for greater flexibility.
Now you have something searchable on your computer that directs you to which notebook (and approximately where in that notebook) to find it.
An alternative is to scan or photograph the pages of your note book and use relevant software to add labels/descriptions to the scanned images. (You can embed all sorts of searchable fields inside jpeg and some other image types - search for information on IPTC or XMP, or I can offer more detail here if you need it.) If you were going to photograph the pages you might set up a little stand to hold your phone the right height to make this quick and easy.
If you end up writing long drafts on paper then treat them like drafts: don't transcribe so much as edit onto the computer (besides, I always think that editing the first draft is much better on paper). Again you can use scans or photos to allow you to backup your drafts until the editing processing is done.
I've used a mixture of these approaches over the years, different approaches for different jobs. I rather like labelling scanned image files as an option, because you get to keep it all on the computer and once the label/description information is attached to the image it can be extracted out into databases for optimised searching or whatever; I've used this for helping to collate family history details.