Alas EWOM - unlike MoM (and that way wasn't perfect, either) - has no way to target a particular unit in a stack. The only workable way to place enchantments is to move the target unit out of the stack.
If I was to wish for a perfect feature, I'd wish for a selection list of the target stack, where illegal units are very visibly crossed out (already has the enchantment, trained unit and imbue...) and mouseover on a unit would foldout a list of the unit's current enchantments.