I believe whether its keyclone, ISBoxer, AHK, Pwn... whatever the multiplexer you use, you are going to have to broadcast your keys to the other client windows. The way you do this with ISBoxer is to

1. establish a WoW keybind IWT. For now, just pick a key, doesnt matter what key, lets use "K". (you must do this for ALL client windows. Make sure all your toons have the same keybind.
2. in ISBoxer, under the DPS1 key, you can choose to use a mapped key "K" and send it to all windows. the options are to use in current window only, or clients only, or all windows.

Thats the VERY VERY cut to the bone description I know how to give. Khatovar give a good detailed explaination. Im glad to see you progressing. Cause it doesnt happen overnight, and BAM! your a multiboxer.