I understand the need to doodle. I am an art teacher and since I was a kid I used to doodle on my notes. I still do. But let me make a suggestion that might work better, and actually be more productive. Since you can switch very easily from window to window how about opening a blank journal file, and switch to that file at the point at which you feel compelled to doodle? Then you can switch back to notes and pdf materials for serious attention. You can switch back and forth as often as you like. The advantage to this is that you keep your notes and pdf materials clean of extraneous doodles, and you also can have an ongoing doodle pad that you add to over the course of the day or even the week if you save it and reopen it.