You need to run it in windowed mode with the 'Maximize Screen' setting set, this makes the window full screen but when you move your cursor to the top the apple bar will pop up.

I'm fairly versed in multiboxing on a mac, so if you have any more questions, ask me. I'm actually currently working on improving the code of clonedkeys in order to get rid of the buffer delay lag issue. I suggest you get cloned keys instead of clonekeys, its much more updated and has more options. As of right now though, I do not box on my mac (well I do, but not under OS X, I use windows 7). The buffer error is just to much of a breaker for me (not being able to span, key presses not being passed through properly etc.)

The current version of clonedkeys was broken in 10.5.6 but here is a patched / fixed version of it.

http://www.snow-okami.net/files/ClonedKeys.zip

Have fun multiboxing!