It's fairly simple - don't use any multiboxing software.

Because EVE is 99% mouse driven I think must of us don't bother using any broadcasting or screen moving software

I just cascade the EVE windows across the screen and switch between them as required (I'm playing EVE in windowed mode of course)

If I had a multimonitor setup I might put some of the windows on other screens but there's usually so little going on (I tend to be mining when multiboxing) hats it's not a problem.

Missions and PVP would be a different matter though... - might need to upgrade to extra screens for that - it all depends on the number of clients you want to run