Note taking when your main screen is being used for class.
My first thought, is why does note taking have to be electronic? Research has shown that taking notes by hand is more effective. So let us model it for our students, and if they ask why, explain it. My overly simplistic explanation is that if you take notes, when it comes in through your ears it has to rattle around in your brain a while before finding its way out through your fingers. Since you can often type without really thinking about it, it didn’t rattle enough. Transcribe to electronic format later.
Next question is are you using an overhead or are you trying to teach from home?
Either way, use a dual screen type model. If you do not have a dual monitor, will switch between open windows. In a room, “extend” your desktop, so you have two different screens, either for the projector and desktop, or one monitor is showing on the desktop.
Trying to remote teach, when you present, present a particular window, not your whole screen. That takes a little practice to get used to.