I'd probably lead with whoever uses mouse based targeting the most.
As in, a Priest can use Mass Dispel but that has to be aimed via the mouse.
Or a Warlock can do the Rain type spell, that also creates a targeting circle and moves where the mouse moves.

Keyclone doesn't really have that strong of a mouse broadcasting feature, so not being able to use that type of an ability is your largest loss with KC.

Either character can lead.
The other will follow.
You could create two leadership macros quite easily.
Both of them focus ToonA on keybind 1 and both focus ToonB on keybind 2.
Follow then is /follow [target=focus].
Both characters then nuke or castsequence at /cast [target=focustarget].
Set your character switch hotkey (to region1/character1 in Keyclone) to the same hotkey in Wow that makes Toon1 both character's focus.

You can go with castsequence, if there is a sequence your character always does.
For example mash '1' and have the warlock do DotA, DotB, DotC, etc.
And the Priest does DotA, DotB or whatever.

Alternatively, match abilities by function of cast time.
Mind Blast and Shadowbolt have similar cast times.
But Mind Blast has a reuse timer, while shadowbolt doesn't.
So maybe the priest has castsequence Mindblast, Another spell, Another spell... while the Warlock has a straight Shadowbolt on that key.
Both are primary nukes, with a casting time... so the toons are both stationary whenever you want to use that key.

You could round-robin things like Fear.
The priest has Psychic Scream (?... haven't played Wow in a while) while the Warlock has Howl of Terror.
You wouldn't want to use both at once, but one after the other would be a bonus to have.