(Assuming Alt-Tab is your key combo for switching focus between windows:)
Alt-Tab is my key combo for *cycling* through windows. I'm still in the habit of clicking with the mouse to give the window the focus, but there's a key combo for it that you can use instead.
That's what I do too, which is exactly what I so clumsily tried to
explain. That leaves one of the windows you want in the master area,
and the other in the non-master area (slave?). Can you then switch
back to the master area *without the window in the non-master area
changing*?
I think I explained it badly. The way I do it, you don't need to switch *back* to the master window because you're already there.
1. Click (or whatever you do to set focus) on master window.
2. Alt-tab (or whatever you do to cycle) as many times as needed to get the window you want in the non-master area.
Now you can click (swap focus) between the master and non-master windows, and they will stay the same.
Tonight when I'm on my normal computer, I'll try to do it entirely mouse-free so I can write better instructions.