Thank you for your responses. Ended up playing with it for a few hours last night and am starting to get used to it. I ended up just binding Q and E for the alt account to make it turn towards the target and this has made things much more bearable. Since I changed character combos to warrior/pally it doesn't really matter if the two are on top of each other, I was just curious how the guy did it.

To answer thinus' question I am using a single 22" WS monitor(1680x1050 res.), with the two WoW windows side by side. I messed around with a couple different configurations and found this one to be the easiest to manage. Unfortunately I don't have another monitor readily accessible to test a multi-monitor setup.