I prefer to take my study notes outside of Logos 4. I have been looking for a system that allows me to:
1. Keep the notes and Logos 4 on the screen at the same time without having to switch via Command-Tab.
2. Sync the notes to my home computer.
3. Have some sort of linking from Logos 4 (So that I know that I have written a note on a particular verse).
4. Not be tied to any special file format that could go obsolete or prevent me from moving to a different computer system someday.
I came across this idea from LaRosa Johnson using Microsoft Onenote, but not having Onenote on the Mac, I developed a similar system to achieve my goals using a Mac app called TextWrangler.
If you are interested, you can have a look at the video that I made (the first few seconds are blank video).
Let me know what you think. I'm also interested if you've developed any other systems for taking notes outside Logos 4.