I use KeyClone, too.

Top priority: Get the Jamba addon if you don't have that already - it really is a godsend for multiboxing.

Other than that, my setup is pretty basic, I have a AHK script that changes master to slave when activating the PiP functions of KeyClone (well, to be specific, it changes the master to a slave, then fires the PiP change). This way, if I press F1, it'll switch my "A" character to the first window, make him the jamba-master, group leader and the focus of the slaves. F2 does it for my "B" character, and so on. It's not a full-on FTL setup, obviously, but it does the job for me. I then use a bunch of macros that have [target=focustarget] in them, so all my toons will fire on the same target no matter what they have selected themselves.