The compositional parameter space in the formation of polynuclear clusters is probed in the synthesis of a series of dodecanuclear coordination clusters of Ni(II) and Co(II) with isostructural D(3h)-symmetric frameworks. At the core of their construction are a carbonate template and the directing ligands cis,trans-1,3,5-triaminocyclohexane and acetate at contrasting pH values. The pH and stoichiometric dependence has been mapped, and analysis by electrospray mass spectrometry reveals the cluster cores in solution. In two specific cases, site-specific occupations are eluded to by analysis of the magnetic properties, and we discuss the possibility of controlling the molecular composition of mixed metal polynuclear clusters.