CueCam Presenter solves this quite elegantly: You can prepare a script with a card for each window you want to share. Then you can just select the card during the presentation and it will share just that window.

I also have a single large screen. So I put the CueCam window on the right, top to bottom. And the windows I want to share in the bottom left quadrant. There I can make them smaller, with the correct aspect ratio, so that participants with smaller screens can see all the detail they need.

That leaves the top left quadrant for my meeting window where I can see the meeting participants.

I'm also experimenting with the two companion apps: Shoot to use my iPhone camera and control zoom from CCP; and Video Pencil to draw on my video.