CloneKeys itself doesn't really have any options or any setup. I've found its really about setting up WoW (and all copies) to make the best use of the limited functionality of CloneKeys.

I laid out my keybindings and explained them in great detail here: Mixed Groups.

Basically, I just have a follow macro for movement and an assist macro to match targets between chars. Then the action bars (spells) are carefully placed so every one casts the same spell (or a spell with a similiar cast time in the case of multiple classes) at the same time. Some exceptions are polymorph and the sometimes I have my priest not cast while my 2 mages are.