Clone Keys Problems

Im new to dual boxing and ive just set up a new free trail account. I made two human locks and made some basic macros. (/follow /assist) the problem is the only way i can get the dual boxing cookin is if i only use the keyboard. Once i set up in the clone keys program window i must keep the clone keys program window up as the active window if i use my mouse to click off onto my main wow window i loose control of the second character. Could someone explain why this isnt working. Im on a new apple macbook pro if that helps.

P.S. what are some more advanced macros and set up tips i should know.

Thanks,

Zulle {sargeras alliance}