I keep my main screen clear by putting option palettes on my second screen, which mostly works perfectly. However, if I have another document open on that second screen, some commands get applied that second-screen document instead of the one I'm currently working on the main screen.

To recreate this: On a 2-screen setup open a document on each screen, working in a document on screen 1 while the Layers Palette is on screen 2 out of the way.

Click the eye symbol to hide a layer and it affects the live document on screen 1, as you'd expect.

Option Click the eye (to hide all other layers), and it switches off those layers on the screen 2 document, not you're actually working on screen 1.